pw.obo

format-version: 1.2
date: 14:10:2013 11:53
saved-by: VPetri
auto-generated-by: OBO-Edit 2.2
synonymtypedef: KEGG "KEGG" RELATED
synonymtypedef: NEWSYNTYPE "<new synonym type>" RELATED
synonymtypedef: PID "PID" RELATED
default-namespace: pathway

[Term]
id: PW:0000000
name: term zero
is_obsolete: true

[Term]
id: PW:0000001
name: pathway
def: "A pathway is a set of inter-connected  reactions and interactions whose delineation and scope are used as a model for exploring and studying, describing and understanding the working of and relationships between biomolecules within a context." []

[Term]
id: PW:0000002
name: classic metabolic pathway
def: "The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics." [OneLook:http\://www.onelook.com/]
comment: The definition was compiled based on a number of available defintions in various dictionaries.
is_a: PW:0000001 ! pathway

[Term]
id: PW:0000003
name: signaling pathway
def: "The pathways where a signal - hormone, neurotransmitter, growth factor, peptide, any molecule - triggers one or multiple cascades of events. This involves a number of molecules, including receptors, proteins, ligands, messengers, any participating molecule. A signaling pathway may be upstream or downstream of other signaling pathways. Signaling pathways control a very broad spectrum of processes as well as pathways." [OneLook:www.onelook.com]
comment: The definition was compiled based on a number of definitions available in various dictionaries.
is_a: PW:0000001 ! pathway

[Term]
id: PW:0000004
name: regulatory pathway
def: "The pathways that control the processes by which a cell or organism develops, adjusts, behaves, responds to conditions or changes in these conditions, or in any manner helps promote and maintain its efficient functioning." [OneLook:www.onelook.com]
comment: The definition was complied based on a number of definitions available in several dictionaries
is_a: PW:0000001 ! pathway

[Term]
id: PW:0000005
name: carbohydrate metabolic pathway
def: "Those metabolic reactions and pathways involved in the oxidation, breakdown and synthesis of carbohydrates in the tissue. The breakdown can be utilized by the body for energy production." [OneLook:www.onelook.com]
comment: The definition  was compiled using the Online Medical dictionary and the Stedman's medical dictionary available at OneLook
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000006
name: Ras superfamily mediated signaling pathway
def: "The Ras superfamily consists of a diverse group of small, monomeric G proteins that function as molecular switches alternating between the GDP-inactive and the GTP-active bound state. The GTP-bound form can interact with many downstream effectors. Ras superfamily controls a broad spectrum of processes; deregulation of Ras cascades has been linked to several forms of cancer. The superfamily is structurally classified in five families." [GO:0007265, PMID:11027944, PMID:1152757]
comment: Numerous articles contributed to this definition, too many to cite independently.
synonym: "monomeric G protein mediated signaling pathway" RELATED []
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000007
name: mitogen activated protein kinase signaling pathway
def: "The mitogen -activated protein kinase pathway groups several serine/threonine protein kinases mediated cascades in response to a number of extracellular stimuli.  A characteristic feature of these cascades is the presence of at least three kinases in series leading to the activation of a multifunctional MAP kinase." [GO:0000165, KEGG:map04010, PMID:14570565, PMID:14976517, PMID:17229475, PMID:17306385, Reactome:REACT_634.5]
synonym: "KEGG:04010" RELATED []
synonym: "MAPK signaling pathway" EXACT []
is_a: PW:0000003 ! signaling pathway
is_a: PW:0001194 ! serine/threonine-specific kinase mediated signaling pathway

[Term]
id: PW:0000008
name: Wnt signaling pathway
def: "The secreted glycoproteins of the Wnt family regulate a wide spectrum of developmental processes and they are also playing important roles in the adult organism. Deregulation of Wnt cascades has oncogenic effects and is responsible for tumorigenesis in adults." [PMID:12573432, PMID:15001769, PMID:15041171]
synonym: "KEGG:04310" RELATED []
is_a: PW:0000650 ! signaling pathway pertinent to development
is_a: PW:0000656 ! glycoprotein signaling pathway

[Term]
id: PW:0000009
name: apoptotic cell death pathway
def: "Apoptosis is a programmed cell death pathway that is characterized by particular morphological features such as membrane blebbing and DNA fragmentation. It can be intrinsic or extrinsic and involves the activation of caspases." [GO:0006915, KEGG:map04210, OneLook:www.onelook.com, PMID:12196263, PMID:18414491]
synonym: "KEGG:04210" RELATED []
synonym: "programmed cell death pathway" RELATED []
is_a: PW:0000275 ! cell death pathway

[Term]
id: PW:0000010
name: lipid metabolic pathway
def: "The metabolic reactions involved in the oxidation, utilization and/or synthesis of lipids in the tissues." [OneLook:www.onelook.com]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000011
name: amino acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of the primary or standard 20 amino acids found in proteins. Amino acids are described as non-essential or essential depending on whether humans can or can not synthesize them, respectively. Chemically, they are classified based on the polarity of their side chain or R group, as non-polar and hydrophobic and hydrophilic and charged or polar uncharged. Amino acid metabolic pathways are also listed with their KEGG entries." [KEGG:http\://www.genome.jp/kegg/, MCW library:Handbooks of Biochemistry]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000012
name: nucleotide metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nucleotides. Nucleotides, which are the units of DNA and RNA, can also play important roles in cellular energy, enzyme regulation as well as serve as signaling molecules." [PMID:20561600, PMID:21222015]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000013
name: disease pathway
def: "Complex human diseases encompass a spectrum of genetic and environmental attributes that together affect the normal functioning of several molecular and cellular pathways. Their combined and accumulated effect is manifested in the anomalous phenotype of the complex condition." [InHouse:InHouse PW dictionary]
synonym: "complex human diseases" RELATED []
is_a: PW:0000001 ! pathway

[Term]
id: PW:0000014
name: neurodegenerative disease pathway
def: "Neurodegenerative diseases group together a number of conditions of various and many times poorly understood origins that are characterized by the progressive loss of particular neurons, the formation of particular structures such as plaques and fibrils, and protein aggregates. Proteosomal degradation, programmed cell death, oxidative stress, are among a number of pathways thought to be disrupted." [inHouse:InHouse PW dictionary]
is_a: PW:0001412 ! nervous system disease pathway

[Term]
id: PW:0000015
name: Alzheimer disease pathway
def: "A mostly sporadic, late-onset condition affecting the central nervous system, is the most prevalent neurodegenerative disease and the most common form of dementia. It is characterized by the presence of amyloid plaques and fibril tangles. Possible pathways affected range from protein misfolding and aggregation, to oxidative stress and impaired metal homeostasis." [InHouse:InHouse PW dictionary, KEGG:map05010]
synonym: "KEGG:05010" RELATED []
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000016
name: amyotrophic lateral sclerosis disease pathway
def: "A late onset, mostly sporadic neurodegenerative disease characterized by the loss of motor neurons in the brain stem and spinal cord. Various pathways are thought to be deregulated and contribute to the condition; among them calcium and/or zinc homeostasis, apoptosis, Cdk5 and calcineurin dependent processes, and in the case of the more rare, genetically inherited form of the disease, mutations in the cytosolic Cu, Zn superoxide dismutase (SOD1) and the subsequent changes in the processes that involve SOD1." [InHouse:In House PW dictionary, KEGG:map05014]
synonym: "ALS pathway" EXACT []
synonym: "KEGG:05014" RELATED []
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000017
name: Huntington disease pathway
def: "An inherited form of a neurodegenerative disease caused by an expanded polyQ (polyglutamine) tract. It mostly affects the striatum and cortex, but extends to other regions later in its development. It manifests itself in movement disorders, psychiatric abnormalities, cognitive defects, and manifold pathways are disrupted." [KEGG:map05016, PubMed:2004\, v.20 (3)\, 146-154.]
synonym: "KEGG:05016" RELATED []
is_a: PW:0000171 ! disease pathways related to polyQ repeats

[Term]
id: PW:0000018
name: Parkinson disease pathway
def: "One of the most common neurodegenerative diseases that is characterized by the loss of dopaminergic neurons  in the substantia nigra and the presence of cytoplasmic inclusions called Lewy bodies in surrounding neurons. Several pathways are thought to be deregulated; for instance, imbalance of iron homeostasis is believed to contribute to the pathogenesis of the condition." [KEGG:map05012, PubMed:2004\, v.101 (15)\, 5500-5505.]
synonym: "KEGG:05012" RELATED []
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000019
name: prion diseases pathway
def: "Prion disease - any of a group of fatal, transmissible neurodegenerative diseases caused by abnormalities of prion protein metabolism, which may result from mutations in the prion protein gene or from infection with pathogenic isoforms of the protein.  Characteristics include neuronal loss, gliosis, and extensive vacuolization of the cerebral cortex. Prion diseases may be sporadic, inherited as an autosomal dominant trait, or acquired. Human diseases include Creutzfeldt-Jakob disease, Gerstmann-Strussler syndrome, fatal familial insomnia, and kuru" [KEGG:map05020, OneLook:www.onelook.com]
synonym: "KEGG:05020" RELATED []
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000020
name: cardiovascular disease pathway
def: "Cardiovascular diseases represent a very broad spectrum of conditions that can also combine with diabetes and renal failure." [InHouse:InHouse PW dictionary]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000021
name: hypertension pathway
def: "Hypertension, high arterial blood pressure: various criteria for its threshold have been suggested, ranging from 140 mm Hg systolic and 90 mm Hg diastolic to as high as 200 mm Hg systolic and 110 mm Hg diastolic. Hypertension may have no known cause (essential or idiopathic h.) or be associated with other primary diseases (secondary h.)." [OneLook:www.onelook.com]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000022
name: cardiomyopathy pathway
def: "Cardiomyopathy - a general diagnostic term designating primary noninflammatory disease of the heart muscle, often of obscure or unknown etiology and not the result of ischemic, hypertensive, congenital, valvular, or pericardial disease. It is usually subdivided into dilated, hypertrophic, and restrictive cardiomyopathy (1). Cardiomyopathy is the deterioration of the cardiac muscle of the heart wall." [OneLook:www.onelook.com]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000023
name: immune response pathway
def: "The Immune response pathways mediate the defense of host cells against infection and injury. The first line of defense is provided by the phylogenetically older innate immune response. The later, more versatile response is provided by the pathways of adaptive immunity: the B cell mediated humoral and the T cell mediated cellular or cell-mediated responses." [GO:0006955, MCW library:Handbook of cellular and molecular immunology, OneLook:www.onelook.com]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000024
name: inflammatory response pathway
def: "Inflammation is the cellular response of the innate immune system to infection or injury. Sensing of infection by pattern recognition receptors triggers signaling cascades leading to the expression of mediator genes such as the pro-inflammatory cytokines." [GO:0006954, MCW library:Cellular and molecular immunology\, by Abbas\, Abul K, OneLook:www.onelook.com, PMID:15364056, PMID:16226680, PMID:16281932, PMID:20303867, PMID:20303872]
synonym: "CLR signaling pathway" RELATED []
relationship: part_of PW:0000234 ! innate immune response pathway

[Term]
id: PW:0000025
name: glycolysis/gluconeogenesis pathway
def: "Those metabolic reactions involved in the energy-yielding conversion of glucose to pyruvate or in the formation of glucose from non-carbohydrate precursors such as pyruvate, lactate, citric acid cycle intermediates, the carbon skeleton of many amino acids. While many enzymes are shared by the two pathways, a few steps are carried out by pathway-specific enzymes. The two pathways are independently regulated." [KEGG:map00010, MCW library:Voet & Voet \"Fundamentals of Biochemistry\" 3rd edition, OneLook:www.onelook.com]
synonym: "KEGG:00010" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000026
name: citric acid cycle pathway
def: "The series of chemical reactions that are central to all aerobic cells and constitute the citric acid cycle. Also known as the tricarboxylic acid cycle (TCA) or Krebs cycle, it is the center of convergence for all molecular fuels." [GO:0006099, KEGG:map00020, OneLook:www.onelook.com, Reactome:REACT_1046.3]
synonym: "KEGG:00020" RELATED []
synonym: "Krebs cycle pathway" RELATED []
synonym: "TCA cycle pathway" RELATED []
synonym: "tricarboxylic cycle pathway" RELATED []
is_a: PW:0000033 ! energy metabolic pathway
relationship: part_of PW:0000357 ! energy homeostasis pathway

[Term]
id: PW:0000027
name: glutamic acid/glutamate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation glutamic acid/glutamate. Glutamate is the major excitatory neurotransmitter." [OneLook:www.onelook.com]
comment: Definition compiled based on the information available for glutamate at OneLook
is_a: PW:0000445 ! excitatory neurotransmitter metabolic pathway
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway

[Term]
id: PW:0000028
name: alanine, aspartate and glutamate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of alanine, aspartate and glutamate." [OneLook:www.onelook.com]
comment: The definition was compiled based on the information on alanine and aspartate available at OneLook.
synonym: "KEGG:00250" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000029
name: fatty acid biosynthetic pathway
alt_id: PW:0000030
def: "Acetyl-CoA, the starting material for fatty acid biosynthesis, can be derived from amino acid and lipid degradation or the oxidative decarboxylation of pyruvate. Fatty acid biosynthesis involves the condensation of C2 units; it requires seven enzymatic reactions which are carried out by the multifunctional enzyme fatty acid synthase." [GO:0006633, KEGG:map00061, MCW Library:Biochemistry Handbook]
synonym: "KEGG:00061" RELATED []
is_a: PW:0000058 ! fatty acid metabolic pathway

[Term]
id: PW:0000031
name: purine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of purines. Purines consist of a pyrimidine ring fused to an imidazole ring. The nucleobases adenine and guanine in DNA are purines." [OneLook:www.onelook.com]
synonym: "KEGG:00230" RELATED []
is_a: PW:0000012 ! nucleotide metabolic pathway

[Term]
id: PW:0000032
name: pyrimidine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of pyrimidines. Cytosine, thymine and uracil - the nucleobases found in nucleic acids, are pyrimidine derivatives." [OneLook:www.onelook.com]
synonym: "KEGG:00240" RELATED []
is_a: PW:0000012 ! nucleotide metabolic pathway

[Term]
id: PW:0000033
name: energy metabolic pathway
def: "Those metabolic reactions and pathways whose role is to release or provide energy." [OneLook:www.onelook.com]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000034
name: electron transport chain pathway
def: "Those metabolic reactions thereby the electrons derived from the oxidation of glucose and lipids or the degradation of amino acids, are passed to oxygen via a series of series of spatially separated complexes. The energy derived generates an electrochemical gradient that drives the synthesis of ATP. The coupling between the electron transport chain, also known as the respiratory chain and the ATP biosynthetic pathway is known as oxidative phosphorylation. Under certain circumstances the two may be uncoupled." [GO:0022904, OneLook:www.onelook.com, PMID:19760284, PMID:21625217]
synonym: "ETC pathway" RELATED []
synonym: "respiratory chain pathway" RELATED []
relationship: part_of PW:0000357 ! energy homeostasis pathway
relationship: part_of PW:0001059 ! oxidative phosphorylation pathway

[Term]
id: PW:0000035
name: ATP biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of adenosine triphosphate (ATP). ATP synthesis is coupled to the electron transfer or respiratory chain pathway which generates an electrochemical gradient that drives the phosphorylation of ADP. The coupling of the two pathways is called oxidative phosphorylation. Under certain circumstances however, the two may be uncoupled." [GO:0006754, OneLook:www.onelook.com, PMID:19760284, PMID:21625217]
relationship: part_of PW:0000357 ! energy homeostasis pathway
relationship: part_of PW:0001059 ! oxidative phosphorylation pathway

[Term]
id: PW:0000036
name: nitrogen metabolic pathway
def: "Those metabolic reactions in the nitrogen cycle carried out by various microorganisms." [KEGG:map00910]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000037
name: sulfur metabolic pathway
def: "Those metabolic reactions involving sulfur - a component of methionine and cysteine amino acids and of co-enzymes and vitamins. It also serves as electron donor in anaerobic respiration. Microorganisms and plants can incorporate inorganic sulfate into bioinorganic compounds; higher organisms derive them from diet." [KEGG:map00920, PMID:16143557, Wikipedia:http\://en.wikipedia.org/wiki/Sulfur_metabolism]
synonym: "KEGG:00920" RELATED []
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000038
name: Sterol, vitamin K, vitamine E and cartenoids  biosynthesis
def: "OBSOLETE. Originally found at KEGG, the term has since been deleted." [PW dictionary:InHouse dictionary]
is_obsolete: true

[Term]
id: PW:0000039
name: bile acid biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of bile acid - any of the steroid carboxylic acids derived from cholesterol. Cholic and chenodeoxycholic acids are the primary bile acids and are formed in the liver. Secondary bile acids - deoxycholic and lithocholic - are formed from the primary bile acids through the action of intestinal bacteria. Bile acid also acts as a signal molecule via several nuclear receptors." [OneLook:www.onelook.com, PMID:22414897]
synonym: "KEGG:00120" RELATED []
is_a: PW:0001304 ! cholesterol metabolic pathway

[Term]
id: PW:0000040
name: steroid hormone biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of steroid hormones. All steroid hormones are derived from cholesterol. Steroid hormone metabolism is extremely complex and its molecular details are incompletely understood. De novo steroid biosynthesis is confined to very few tissues, primarily the adrenals, the gonads and the placenta." [KEGG:map00140, OneLook:www.onelook.com, PMID:17926129]
synonym: "KEGG:00140" RELATED []
is_a: PW:0001152 ! steroid biosynthetic pathway
is_a: PW:0001305 ! steroid hormone metabolic pathway

[Term]
id: PW:0000041
name: fructose and mannose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of fructose and mannose, as depicted in the KEGG diagram." [KEGG:map00051, OneLook:www.onelook.com]
synonym: "KEGG:00051" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000042
name: galactose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of galactose - an aldohexose epimeric with glucose at the 4 carbon. Galactose is a component of lactose and other oligosaccharides, cerebrosides and gangliosides, and of various glycolipids and glycoproteins." [GO:0006012, KEGG:map00052, OneLook:www.onelook.com]
synonym: "KEGG:00052" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000043
name: pyruvate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of pyruvate - a salt, ester, or anionic form of pyruvic acid. Pyruvate, which is the end-product of glycolysis can be converted to lactate under anaerobic conditions, can be further oxidized via the Krebs or citrate cycle or can be converted back to glucose via gluconeogenesis." [GO:0006090, KEGG:00620, OneLook:www.onelook.com, Reactome:REACT_2071.3]
synonym: "KEGG:00620" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway
is_a: PW:0000556 ! glucose oxidation pathway

[Term]
id: PW:0000044
name: Duplicated Glutamate Metabolism term
def: "OBSOLETE. Duplicated term. Use PW:0000027." [PW dictionary:InHouse dictionary]
is_obsolete: true

[Term]
id: PW:0000045
name: pentose phosphate pathway
def: "Those metabolic reactions involved in the generation of reducing equivalents and five carbon (pentose) sugars. The oxidative phase is irreversible; the non-oxidative is reversible." [GO:0006098, KEGG:map00030, OneLook:www.oneloook.com, Reactome:REACT_1859.1]
synonym: "hexose monophosphate pathway (shunt)" RELATED []
synonym: "KEGG:00030" RELATED []
synonym: "pentose phosphate shunt" RELATED []
synonym: "phosphogluconate pathway" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000046
name: inositol metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of inositol, a cyclic sugar alcohol occurring in a number of stereoisomers of which the myo-inositol is the most prominent form. myo-inositol provides a structural basis for compounds such as inositol phosphates and phosphatidylinositols  which are secondary messengers in several signaling pathways." [GO:0006020, OneLook:www.onelook.com]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000047
name: glycine, serine and threonine metabolic pathway
def: "Those metabolic reactions involved in the synthesis of glycine, serine and threonine and which are intimately connected with serine being synthesized from glycine and threonine." [OneLook:www.onelook.com]
comment: Definition compiled based on the information available at oneLook
synonym: "KEGG:00260" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000048
name: methionine cycle/metabolic pathway
def: "Those metabolic reactions involved in the synthesis (remethylation), utilization and/or degradation of methionine, an essential amino acid for humans. The cycle produces S-adenosylmethionine (AdoMet),  the major methyl donor for proteins, nucleic acids, lipids and other small molecules. The cycle also produces homocysteine (Hcy) which either regenerates methionine via the  remethylation pathway or leads to the synthesis of cysteine and derivatives via the transsulfuration pathway. Homocysteine and folate metabolic pathways are intimately related to the methionine cycle." [MCW library book:Homocysteine in Health and Disease]
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway

[Term]
id: PW:0000049
name: cysteine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of cysteine, a non-essential amino acid that could be essential in certain cases. Its side chain contains a sulfhydryl group that is readily oxidized to form the cystine dimer covalently linked by a disulfide bond." [OneLook:www.onelook.com]
comment: Reference compiled based on the information available at OneLook for cysteine.
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway

[Term]
id: PW:0000050
name: arginine and proline metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of arginine - an essential amino acid - and proline - an amino acid that can play important roles in protein secondary structure." [OneLook:www.onelook.com]
comment: Definition compiled based on the information on arginine and proline available at OneLook
synonym: "KEGG:00330" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000051
name: histidine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of histidine, an essential amino acid which can act as either a proton donor or a proton acceptor." [OneLook:www.onelook.com]
synonym: "KEGG:00340" RELATED []
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000052
name: tyrosine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of tyrosine - a nonessential amino acid produced from phenylalanine and precursor of thyroid hormones, catecholamines and melanin. Along with phenylalanine and tryptophan is one of the three aromatic amino acids." [wikipedia:http\://en.wikipedia.org/wiki/Tyrosine]
synonym: "KEGG:00350" RELATED []
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000053
name: phenylalanine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of phenylalanine, an essential amino acid. Along with tyrosine and tryptophan is one of the three aromatic amino acids." [OneLook:www.onelook.com]
synonym: "KEGG:00360" RELATED []
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000054
name: tryptophan metabolic pathway
def: "Those metabolic reactions that are involved in the synthesis, utilization and/or degradation of tryptophan - a dietary essential amino acid and precursor for several important compounds. Along with phenylalanine and tyrosine is one of the three aromatic amino acids." [wikipedia:http\://en.wikipedia.org/wiki/Tryptophan]
synonym: "KEGG:00380" RELATED []
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000055
name: nucleotide sugar metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nucleotide sugars. Nucleotide sugars are glycosyl donors usually classified depending on the type of the nucleoside forming them. Several are used in animals and many others can be found in plants and bacteria." [InHouse:PW dictionary, KEGG:map00520]
synonym: "KEGG:00520" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000056
name: photosynthesis pathway
def: "A chemical combination caused by the action of light; specifically the formation of carbohydrates (with release of molecular oxygen) from carbon dioxide and water in the chlorophyll tissue of plants and blue-green algae under the influence of light. In bacteria, photosynthesis employs hydrogen sulfide, molecular hydrogen, and other reduced compounds in place of water, so that molecular oxygen is not released." [GO:0015979, OneLook:www.onelook.com]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000057
name: carbon fixation pathway
def: "The pathway thereby photosynthetic organisms such as plants and cyanobacteria convert inorganic carbon (usually carbon dioxide) into organic compounds (usually carbohydrates)." [OneLook:www.onelook.com]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000058
name: fatty acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of fatty acids - any long-chain monobasic organic acid." [GO:0006631, KEGG:map00071]
synonym: "KEGG:00071" RELATED []
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000059
name: signaling pathway pertinent to the brain
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000060
name: long term potentiation
def: "Long-term potentiation (LTP) is a strengthening of the synapse that can last from hours to days and months.  It is thought to underlie information storage and constitute the cellular basis of learning and memory.  LTP engages numerous cascades of events on either side of the synapse and is accompanied by changes in gene expression." [Dorland's:www.onelook.com, GO:0060291, KEGG:map04720]
synonym: "KEGG:04720" RELATED []
synonym: "LTP" EXACT []
relationship: part_of PW:0000455 ! excitatory synaptic transmission pathway

[Term]
id: PW:0000061
name: long term depression
def: "Long term depression is a weakening of a synapse that lasts hours to days. It results from either strong synaptic stimulation (as in the cerebellum) or to weak synaptic stimulation (as in the hippocampus), and engages several cascades." [GO:0060292, KEGG:map04730, OneLook:www.onelook.com]
comment: Adapted from Wikipedia at OneLook
synonym: "KEGG:04730" RELATED []
synonym: "LTD" EXACT []
relationship: part_of PW:0000455 ! excitatory synaptic transmission pathway

[Term]
id: PW:0000062
name: ascorbate and aldarate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of ascorbate and aldarate, as depicted in the KEGG diagram." [KEGG:map00053, OneLook:www\,onelook.com]
synonym: "KEGG:00053" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000063
name: glyoxylate and dicarboxylate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glyoxylate and dicarboxylate, as depicted in the KEGG diagram." [KEGG:map00630, OneLook:http\://www.onelook.com]
synonym: "KEGG:00630" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000064
name: propanoate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of propanoate - any salt or ester of propanoic or propionic acid. Several propanoates are used in the food industry." [KEGG:map00640, OneLook:www.onelook.com, Web:http\://dl.clackamas.cc.or.us/ch106-04/nomencla1.htm]
synonym: "KEGG:00640" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000065
name: butanoate metabolic pathway
def: "Those reactions involved in the synthesis, utilization and/or degradation of butanoate - an ester or salt of  n-Butyric acid. Various butanoates are used as ingredients in flavoring and perfumery." [KEGG:map00650, OneLook:www.onelook.com]
synonym: "KEGG:00650" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000066
name: C5-branched dibasic acid metabolic pathway
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000067
name: reductive carboxylate cycle - CO2 fixation pathway
def: "Those reactions involved in carbon dioxide fixation - the reductive carboxylate cycle (CO2 fixation) - the conversion of atmospheric carbon dioxide to organic carbon compounds, as in photosynthesis." [KEGG:map00720, OneLook:www.onelook.com]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000068
name: methane metabolic pathway
def: "Those pathways used by methanotrophs and the methanogens that metabolize methane as the sole carbon source or as byproduct." [GO:0015947, KEGG:map00680, OneLook:www.onelook.com]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000069
name: ketone bodies metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization or degradation of ketone bodies. The chemicals acetoacetate, acetone and beta-hydroxybutyrate are collectively known as ketone bodies, although only the first two are ketones. They provide fuel for heart and skeletal muscle and for the brain during starvation. Excessive accumulation of these acidic chemicals leads to dangerous diabetic conditions known as ketoacidosis." [GO:0046950, KEGG:map00072, MCW Libraries:QU4 V876f 2008, OneLook:www.onelook.com, Reactome:REACT_1861.3]
comment: The definition was compiled using the information from a number of biological/medical dictionaries available at OneLook
synonym: "KEGG:00072" RELATED []
is_a: PW:0000058 ! fatty acid metabolic pathway

[Term]
id: PW:0000070
name: C21-steroid hormone biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of C21-steroid hormones. Pregnenolone, the first C21 steroid derived from cholesterol, and progesterone, to which pregnenolone can be converted, provide the starting material for the biosynthesis of C21, C19 and C18 steroid hormones. The C21 class includes glucocorticoids such as cortisol and mineralocorticoids such as aldosterone. Glucocorticoids and mineralocorticoids are collectively referred to as corticosteroids." [KEGG:map00140, PMID:17926129]
synonym: "corticosteroid biosynthetic pathway" RELATED []
is_a: PW:0000040 ! steroid hormone biosynthetic pathway

[Term]
id: PW:0000071
name: valine, leucine and isoleucine degradation pathway
def: "Those metabolic reactions involved in the degradation of valine, leucine and isoleucine - the three, dietary essential, branched amino acids." [OneLook:www.onelook.com]
synonym: "KEGG:00280" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000072
name: valine, leucine and isoleucine biosynthetic pathway
def: "Those metabolic pathways involved in the synthesis of valine, leucine and isoleucine - the three, dietary essential, branched amino acids." [OneLook:www.onelook.com]
synonym: "KEGG:00290" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000073
name: lysine degradation pathway
def: "Those metabolic reactions involved in the degradation of lysine." [OneLook:www.onelook.com]
synonym: "KEGG:00310" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000074
name: lysine biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of lysine - an essential amino acid." [OneLook:www.onelook.comOnline collection of dictionaries]
synonym: "KEGG:00300" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000075
name: phenylalanine, tyrosine and tryptophan biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of phenylalanine, tyrosine and tryptophan and which are intimately related. Although the body can not manufacture phenylalanine on its own, phenylalanine is the precursor of tyrosine. Phenylalanine together with tryptophan governs the release of an intestinal hormone - cholecystokinin." [OneLook:www.onelook.com]
synonym: "KEGG:00400" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)

[Term]
id: PW:0000076
name: urea cycle pathway
def: "The series of metabolic reactions, occurring in the liver, by which the ammonia derived from the breakdown of amino acids combines with carbon dioxide to form urea." [OneLook:www.onelook.com]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000077
name: beta-alanine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of beta-alanine. Beta-alanine is an amino acid formed in vivo by the degradation of dihydrouracil and carnosine. Beta-alanine is not used in the synthesis of proteins but is a component of natural peptides, vitamins such as vitamin B5 and of coenzyme. A rare genetic disorder, hyper-beta-alaninemia, has been reported." [GO:0019482, KEGG:map00410, Onelook:www.onelook.com]
synonym: "KEGG:00410" RELATED []
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000078
name: cyanoamino acid metabolic pathway
def: "Those metabolic reactions involving cyanoamino acid, amino acid derivatives that contain a cyanide group." [GO:0033052, KEGG:map00460]
synonym: "KEGG:00460" RELATED []
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000079
name: Duplicated Selenoamino acid metabolism term
def: "OBSOLETE. Duplicated term. Use PW:0000133" [PW dictionary:InHouse dictionary]
is_obsolete: true

[Term]
id: PW:0000080
name: Duplicated term - Selenoamino acid metabolism
def: "OBSOLETE. Duplicated term. Use PW:0000133" [PW dictionary:InHouse dictionary]
is_obsolete: true

[Term]
id: PW:0000081
name: D-glutamine and D-glutamate metabolic pathway
def: "Those metabolic reactions involving D-glutamine and D-glutamate as depicted in the KEGG diagram. D-glutamic acid is naturally found primarily in the cell wall of certain bacteria." [Human Metabolome Database:HMDB03339, KEGG:map00471]
synonym: "KEGG:00471" RELATED []
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000082
name: D-arginine and D-ornithine metabolic pathway
def: "Those metabolic reactions involving D-arginine and D-ornithine as depicted in the KEGG diagram." [KEGG:map00472]
synonym: "KEGG:00472" RELATED []
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000083
name: D-alanine metabolic pathway
def: "Those metabolic reactions involving D-alanine, the D-enantiomer of alanine. D-alanine can be found in bacterial cell wall and in some peptide antibiotics." [OneLook:http\://www.onelook.com]
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000084
name: Duplicated glutathione metabolism term
def: "OBSOLETE. Duplicated term. Use PW:0000134" [PW dictionary:InHouse dictionary]
is_obsolete: true

[Term]
id: PW:0000085
name: pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
def: "Those pathways involved in and/or controlling DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis." [Handbook:Handbook of Biochemistry]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000086
name: cell cycle pathway, mitotic
def: "The series of events, collectively known as the cell cycle, that underlie the replication of the genome and the segregation of chromosomes into daughter cells. The cycle begins with a diploid cell and produces two identical diploid cells." [GO:0000278, Handbook:Essential Cell Biology, KEGG:map04110, Reactome:REACT_152.3]
comment: Adapted from  O'Connell and Walwarth, Genome KnowledgeBase
synonym: "KEGG:04110" RELATED []
is_a: PW:0001317 ! cell cycle pathway

[Term]
id: PW:0000087
name: G1 phase pathway
def: "The series of events underlying the progression of early cell cycle into the G phase and under the control of D-type cyclins together with Cdk4 and Cdk6. The formation of the pre-initiation replication complex takes place during this phase." [Reactome:REACT_1590.1, Reactomee:www.reactome.org]
relationship: part_of PW:0000086 ! cell cycle pathway, mitotic

[Term]
id: PW:0000088
name: G1/S transition pathway
def: "The series of events underlying the transition from G1 into S phase and under the control of Cyclin E - Cdk2 complexes." [Reactome:REACT_1783.2, reactome:www.reactome.org]
relationship: part_of PW:0000086 ! cell cycle pathway, mitotic

[Term]
id: PW:0000089
name: S phase pathway
def: "The series of events underlying duplication of the hereditary material of the cell, formation of two copies of the chromosome." [Reactome:REACT_899.3, Reactome:www.reactome.org]
relationship: part_of PW:0000086 ! cell cycle pathway, mitotic

[Term]
id: PW:0000090
name: G2 phase pathway
def: "The series of events underlying the second 'gap' phase of the mitotic cell cycle - an interval between the completion of DNA synthesis and the beginning of mitosis and during which protein synthesis occurs." [Reactome:REACT_1915.2, Reactome:www.reactome.org]
relationship: part_of PW:0000086 ! cell cycle pathway, mitotic

[Term]
id: PW:0000091
name: G2/M transition pathway
def: "The series of events underlying the transition from the G2 phase into mitosis." [Reactome:REACT_2203.2, Reactome:www.reactome.org]
relationship: part_of PW:0000086 ! cell cycle pathway, mitotic

[Term]
id: PW:0000092
name: M phase pathway
def: "The series of events underlying mitosis (M-phase), in turn comprised of several phases, involving nuclear division and cytokinesis and resulting in the formation of two daughter cells." [Reactome:REACT_910.1, Reactome:www.reactome.org]
relationship: part_of PW:0000086 ! cell cycle pathway, mitotic

[Term]
id: PW:0000093
name: M/G1 transition pathway
def: "The series of events underlying progression out of mitosis and division into two daughter cells. It requires the inactivation of cyclinB-cdc2 by the ubiquitin-dependent proteolysis." [Reactome:REACT_1725.1, Reactome:www.reactome.org]
relationship: part_of PW:0000086 ! cell cycle pathway, mitotic

[Term]
id: PW:0000094
name: cell cycle checkpoint pathway
def: "Those pathways involved in the control of cell cycle progression as well as its precision and fidelity." [GO:0000075, PMID:14644189, Reactome:REACT_1538.1]
relationship: part_of PW:0001317 ! cell cycle pathway

[Term]
id: PW:0000095
name: G1/S DNA damage checkpoint pathway
def: "Those pathways of DNA damage response that occur during the G1 phase." [InHouse:PW dictionary, Reactome:REACT_1538.1]
is_a: PW:0000094 ! cell cycle checkpoint pathway

[Term]
id: PW:0000096
name: G2/M checkpoint pathway
def: "Those pathways that assure the genome is replicated only once per cell cycle. The checkpoints control for damaged and un-replicated DNA." [InHouse :PW dictionary, Reactome:REACT_828.2]
is_a: PW:0000094 ! cell cycle checkpoint pathway

[Term]
id: PW:0000097
name: mitotic spindle checkpoint pathway
def: "The pathway prevents cells with mis-aligned chromosomes from dividing. Defects of kinetochore function activate checkpoint proteins to initiate a cascade of events that eventually prevent separation of sister chromatid." [InHouse:PW dictionary, Reactome:REACT_2137.2]
is_a: PW:0000094 ! cell cycle checkpoint pathway

[Term]
id: PW:0000098
name: DNA replication pathway
def: "DNA replication takes place in the context of the cell cycle during the S-phase. The fast and accurate replication of DNA requires the presence and the coordinated function of a complex of proteins known as the replisome. The exact composition of the replisome in higher organisms still has to be fully determined." [OneLook:http\://www.onelook.com, PMID:19665592]
synonym: "KEGG:03030" RELATED []
relationship: part_of PW:0000086 ! cell cycle pathway, mitotic

[Term]
id: PW:0000099
name: DNA repair pathway
def: "The pathways involved in the repair of damaged DNA. The damage can involve mismatched or damaged bases, distortion of the helix or breaks in the DNA double strand. Repair of DNA lesions along with the upstream lesion  detection and signaling its presence are collectively known as the DNA damage response." [GO:0006281, PMID:19847258, Reactome:REACT_216.1]
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
relationship: part_of PW:0001360 ! DNA damage response pathway

[Term]
id: PW:0000100
name: transcription pathway
def: "The pathways governing and/or regulating DNA transcription and gene expression. DNA transcription into coding and non-coding RNA is accomplished by one prokaryotic and several eukaryotic RNA polymerases. Transcription-coupled repair handles DNA lesion that interfere with the progression of RNA polymerases. Splicing of nascent RNA is thought to be predominantly co-transcriptional. Signaling pathways mediated by various transcription factors are involved in the regulation of gene expression." [PubMed:Several articles, wikipedia:http\://en.wikipedia.org/wiki/Transcription]
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis

[Term]
id: PW:0000101
name: translation pathway
def: "The series of events governing the processes thereby mRNA is translated into a polypeptide chain. Post-translational modifications often accompany the formation of the final, mature protein." [GO:0006412, InHouse:InHouse PW dictionary]
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis

[Term]
id: PW:0000102
name: the extracellular signal-regulated Raf/Mek/Erk signaling pathway
def: "The Raf/Mek/Erk signaling pathway - a Ras activated protein kinase cascade - regulates diverse processes such as cell growth, proliferation and differentiation, in response to cytokines, hormones, growth factors." [GO:0070371, KEGG:map04010, PMID:15035987, PMID:17112607, PMID:17229475, PMID:17306385, Reactome:REACT_1482.4, Reactome:REACT_962.4]
is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway
is_a: PW:0000525 ! Ras mediated signaling pathway

[Term]
id: PW:0000103
name: transport pathway
def: "A pathway that mediates or facilitates the movement of biochemical material, organic and inorganic substances and/or drugs." [OneLook\, PubMed\, Online:http\://www.ncbi.nlm.nih.gov/; www.google.com]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000104
name: intrinsic apoptotic pathway
def: "The apoptotic pathway involving organelles, primarily the mitochondrion and endoplasmic reticulum (ER), and involving the pro and anti-apoptotic members of the Bcl family of proteins, cytochrome c, formation of the apoptosome and activation of caspases." [KEGG:map04210, PMID:14744432, Reactome:REACT_964.1]
comment: The reference was compiled based on the information available in the cited article.
is_a: PW:0000009 ! apoptotic cell death pathway

[Term]
id: PW:0000105
name: Rho/Rac/Cdc42 mediated signaling pathway
def: "Members of the Ras related Rho family of proteins control diverse processes such as actin cytoskeletal rearrangements, morphogenesis of dendritic spines, gene expression. Of note is the fact that cytoskeletal rearrangements, primarily actin remodeling have a role to play in vesicular trafficking, a process regulated by Rab proteins." [PMID:11075828, PMID:11152757, PMID:18171430, PMID:8973630]
is_a: PW:0000006 ! Ras superfamily mediated signaling pathway

[Term]
id: PW:0000106
name: extrinsic apoptotic pathway
def: "The apoptotic pathway involving the death receptors mediated route of caspase activation. Members of tumor necrosis superfamily such as the better known Tnf-alpha (Tnf), Fas ligand or Trail elicit apoptosis via receptor associated adapters." [KEGG:map04210, PMID:14744432, Reactome:REACT_1059.1]
synonym: "death receptor mediated apoptotic pathway" RELATED []
is_a: PW:0000009 ! apoptotic cell death pathway

[Term]
id: PW:0000107
name: xenobiotics biodegradation pathway
def: "Those reactions involved in the breaking down of toxic chemical compounds such as oil spills, solvents, pesticides and other pollutants. These chemicals are generally resistant to degradation, but microorganisms possess enzymes that are capable of breaking them down." [KEGG:http\://www.genome.jp/kegg/pathway.html#xenobiotics]
is_a: PW:0001229 ! xenobiotic metabolic pathway

[Term]
id: PW:0000108
name: caprolactam degradation pathway
def: "Those enzymatic reactions involved in the degradation of caprolactam - a cyclic amide of caproic acid used to produce a type of nylon." [GO:0019384, KEGG:map00930, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000109
name: bisphenol A degradation pathway
def: "Those enzymatic reactions involved in the degradation of bisphenol A, known as BPA, an important compound in the production of plastics. However, it is believed to be hazardous to humans and reports have linked several health effects to levels of BPA exposure." [GO:0043636, KEGG:map00363, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000110
name: toluene and xylene degradation pathway
def: "Those enzymatic reactions involved in the degradation of toluene and xylene. Toluene is used as organic solvent in rubber, paint, cement. Xylene represents any of three benzene derivatives used as solvent in printing, rubber, also as a cleaning agent." [KEGG:map00622, Onelook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000111
name: gamma-hexachlorocyclohexane degradation pathway
def: "Those enzymatic reactions involved in the degradation of gamma-hexachlorocyclohexane,  also known as lindane, used as an insecticide and suspected to be carcinogenic." [KEGG:map00361, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000112
name: 3-chloroacrylic acid degradation pathway
def: "Those enzymatic reactions involved in the degradation of 3-chloroacrylic acid." [KEGG:map00641, Online:Various sources]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000113
name: atrazine degradation pathway
def: "Those enzymatic reactions involved in the degradation of atrazine - a herbicide used to kill weeds." [GO:0019381, KEGG:map00791, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000114
name: benzoate degradation pathway via hydroxylation
def: "Those enzymatic reactions involved in the aerobic pathway of benzoate degradation." [GO:0043640, KEGG:map00362, Online :Appl. Env. Microbiology\, 2004\, v.70(9)\, p4861-70.]
is_a: PW:0000282 ! benzoate degradation pathway

[Term]
id: PW:0000115
name: benzoate degradation pathway via CoA ligation
def: "Those enzymatic reactions involved in the anaerobic pathway of benzoate degradation." [GO:0010128, KEGG:map00632, Online:http\://umbbd.ahc.umn.edu/benz/benz_map.html]
is_a: PW:0000282 ! benzoate degradation pathway

[Term]
id: PW:0000116
name: carbazole degradation pathway
def: "Those enzymatic reactions involved in the degradation of carbazole - a crystalline, slightly basic cyclic compound found in anthracene. It reacts with carbohydrates and is used for assay and analysis of carbohydrates and in making dyes." [GO:0046232, KEGG:map00629, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000117
name: fluorene degradation pathway
def: "Those enzymatic reactions involved in the degradation of fluorene - a colorless, crystalline hydrocarbon. It is obtained from coal tar and used in making dyes." [GO:0019429, KEGG:map00628, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000118
name: ethylbenzene degradation pathway
def: "Those enzymatic reactions involved in the degradation of ethylbenzene - a liquid hydrocarbon used in the manufacture of styrene and as a solvent and diluent for dyes and paints." [KEGG:map00642, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000119
name: nitrobenzene degradation pathway
def: "Those enzymatic reactions involved in the degradation of nitrobenzene - an organic compound that occurs either as yellow crystals or yellow liquid used in the manufacture of aniline. It is a poisonous derivative of benzene." [OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000120
name: styrene degradation pathway
def: "Those enzymatic reactions involved in the degradation of styrene - an aromatic hydrocarbon that is colorless and oily. It is used in the manufacture of rubber, resins, plastics. It is a toxic, possibly carcinogenic substance." [GO:0042207, KEGG:map00643, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000121
name: tetrachloroethene degradation pathway
def: "Those enzymatic reactions involved in the degradation of tetrachloroethene - (acetylene tetrachloride) used as solvent for fats, waxes, resins and intermediate in the synthesis of chlorinated hydrocarbons." [KEGG:map00625, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000122
name: Hedgehog signaling pathway
def: "The Hedgehog signaling pathway (Hh) plays important roles in vertebrate embryogenesis, particularly in the differentiation of the neural tube, in vasculogenesis and angiogenesis. Post-embryonically it is believed to play a homeostatic role in the maintenance of stem cells. Alteration of the pathway has been implicated in a number of human cancers." [GO:0007224, KEGG:map04340, PMID:12495844, PMID:15205520, PMID:15596107]
synonym: "KEGG:04340" RELATED []
synonym: "PID:200168" RELATED []
synonym: "PID:200172" RELATED []
is_a: PW:0000650 ! signaling pathway pertinent to development
relationship: part_of PW:0000660 ! hematopoiesis pathway

[Term]
id: PW:0000123
name: synaptic vesicle endocytosis and recycling pathway
def: "The pathway of synaptic vesicle endocytosis and neurotransmitter refill following exocytosis." [PMID:15217342]
is_a: PW:0001072 ! synaptic vesicle cycle pathway

[Term]
id: PW:0000124
name: cellular detoxification pathway
def: "A pathway triggered by exogenous or endogenous elements, compounds or molecules that can be harmful to the system. The phase I (oxidative) and phase II (conjugative) metabolizing enzyme and the phase III transport systems and other pathways are involved in the response mechanisms resulting in processing and subsequent elimination or inducing other downstream effects such as various cell death or inflammatory response pathways." [PharmGKB:http\://www.pharmgkb.org/, PMID:15252150, PMID:17482904, Reactome:REACT_13433.1]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000125
name: G protein mediated signaling pathway
def: "G-proteins act as signal transducers between effectors and receptors; they function as molecular switches alternating between the GDP-inactive and GTP-active bound state. Many types of signals are received by the members of a large superfamily of receptors that then activate distinct G-proteins which route the signal to many and distinct intracellular signaling pathways." [GO:0007186, PubMed:Science\, 2002\, v296\, p1636-39, Reactome:REACT_14797.1]
synonym: "heterotrimeric G protein mediated signaling pathway" RELATED []
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000126
name: RNA polymerase I transcription pathway
def: "The series of events governing the synthesis of ribosomal RNA (rRNA)." [GO:0006360, InHouse:PW dictionary, Reactome:REACT_1309.1]
is_a: PW:0001275 ! eukaryotic RNA polymerase transcription pathway

[Term]
id: PW:0000127
name: RNA polymerase II transcription pathway
def: "The series of events governing the synthesis of messenger RNA (mRNA), most microRNA (miRNA) and other non-protein coding transcripts." [GO:0006366, Reactome:REACT_1366.1, Wikipedia:http\://en.wikipedia.org/wiki/Transcription_%28genetics%29]
is_a: PW:0001275 ! eukaryotic RNA polymerase transcription pathway

[Term]
id: PW:0000128
name: RNA polymerase III transcription pathway
def: "The series of events governing the synthesis of transport/transfer RNA (tRNA)." [GO:0006383, InHouse:PW dictionary, Reactome:REACT_1371.1]
is_a: PW:0001275 ! eukaryotic RNA polymerase transcription pathway

[Term]
id: PW:0000129
name: base excision repair pathway
def: "Base excision repair pathway involves the identification and removal of the damaged base followed by its replacement with the correct nucleotide and ligation of the break in the strand." [GO:0006284, KEGG:map03410, OneLook:www.onelook.com, Reactome:REACT_1104.1]
synonym: "BER pathway" EXACT []
synonym: "KEGG:03410" RELATED []
is_a: PW:0000661 ! single-strand DNA repair pathway

[Term]
id: PW:0000130
name: nucleotide excision repair pathway
def: "Nucleotide excision repair pathway is an important mechanism for the detection of helix distorting base alterations. Unlike the base excision repair pathway that only removes the damaged bases, the NER pathway removes an entire lesion containing segment. The single-strand gap thus introduced is filled in by DNA polymerase using the undamaged strand as a template. The pathway can be subdivided into two sub-pathways: the transcription-coupled and the global genome repair. They only differ in the lesion recognition step while the core repair component is common." [GO:0006289, KEGG:map03420, OneLook:www.onelook.com, PMID:23046879, PMID:23085398, Reactome:REACT_1826.2]
synonym: "KEGG:03420" RELATED []
synonym: "NER pathway" EXACT []
is_a: PW:0000661 ! single-strand DNA repair pathway

[Term]
id: PW:0000132
name: metabolic pathway of other amino acids
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of amino acids other than the common 20 amino acids found in protein. Some of these amino acids like carnitine or homocysteine derive from primary amino acids." [InHouse:PW InHouse dictionary]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000133
name: selenoamino acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of selenoamino acid - an amino acid in which a selenium atom replaces a sulfur atom. Examples include selenocysteine, selenohomocysteine and selenomethionine." [KEGG:map00450, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00029/pathway, Technical glossary:http\://morelife.org/glossary/]
synonym: "KEGG:00450" RELATED []
synonym: "selenocompound metabolic pathway" RELATED []
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000134
name: glutathione metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glutathione - a tripeptide that acts as an antioxidant and provides protection against reactive oxygen species. It is also used in the conjugation of xenobiotics and drugs by the phase II biotransformation enzymes." [GO:0006749, KEGG:map00480, OneLook:www.onelook.com]
synonym: "KEGG:00480" RELATED []
is_a: PW:0000132 ! metabolic pathway of other amino acids
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000135
name: metabolic pathway of cofactors, vitamins, nutrients
def: "Those reactions involved in the synthesis, utilization and/or degradation of cofactors, vitamins and other nutrients. Cofactors are necessary for the proper function of certain proteins and enzymes; they can be inorganic such as the metals ions or the iron-sulfur cluster or organic. Organic compounds that are tightly bound to proteins are also referred to as prosthetic groups. Often, they are or are made from vitamins, compounds that are vital but in small amounts and which are insufficiently synthesized by the organism. Some of these molecules can also perform signaling functions." [OneLook:http\://www.onelook.com]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000136
name: thiamine metabolic pathway
def: "Those metabolic reactions involving thiamine, a water-soluble vitamin of the B complex. It is synthesized in bacteria, fungi and plants while animals obtain thiamine from food. Thiamine insufficiency results in a condition called beriberi." [GO:0006772, KEGG:map00730, OneLook:www.onelook.com]
synonym: "KEGG:00730" RELATED []
synonym: "vitamin B1 metabolic pathway" EXACT []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000137
name: riboflavin metabolic pathway
def: "Those metabolic reactions involving riboflavin, also known as vitamin B2 - a water-soluble vitamin. B12 occurs in several products and is a precursor for flavin coenzymes." [GO:0006771, KEGG:map00740, OneLook:www.onelook.com]
synonym: "KEGG:00740" RELATED []
synonym: "vitamin B2 metabolic pathway" EXACT []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000138
name: vitamin B6 metabolic pathway
def: "Those metabolic reactions involving vitamin B6 - a water-soluble vitamin that exists in several forms. Vitamin B6 is required for many enzymatic reactions and plays important roles in monoamine and protein synthesis. A number of organisms can carry out de novo synthesis of vitamin B6; humans derive it from diet." [GO:0042816, KEGG:map00750, OneLook:www.onelook.com]
synonym: "KEGG:00750" RELATED []
synonym: "pyridoxine metabolic pathway" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000139
name: biotin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of biotin, also known as vitamin B7 or H, a water-soluble vitamin. Biotin assists in various metabolic reactions and processes." [GO:0006768, KEGG:map00780, OneLook:www.onelook.com>, Reactome:REACT_11153.3]
synonym: "KEGG:00780" RELATED []
synonym: "vitamin B7 metabolic pathway" EXACT []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000140
name: folate metabolic pathway
def: "Folate metabolism represents the various aspects of folate cycle and the folate mediate transfer reactions essential for several biosynthetic pathways. The folate cycle and the folate mediated one-carbon pathways are part of folate metabolism. Folate compounds are water-soluble forms of vitamin B9." [PMID:11001804, PMID:15166809, PMID:15298442]
synonym: "KEGG:00790" RELATED []
synonym: "vitamin B9 metabolic pathway" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000141
name: retinol metabolic pathway
def: "Those reactions involving retinol, a fat-soluble vitamin that is the dietary form of vitamin A and is important for bone growth and in vision. Precursors of retinol such as carotenoid or retinyl esters are derived from diet and are converted to retinal and retinol, respectively." [GO:0042572, KEGG:map00830, OneLook:www.onelook.com, PMID:21586336, PMID:21718801]
synonym: "KEGG:00830" RELATED []
is_a: PW:0001003 ! retinoid metabolic pathway

[Term]
id: PW:0000142
name: ubiquinone biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of ubiquinone, also known as coenzyme Q. Ubiquinone is a member of the mitochondrial respiratory chain and plays important roles in cellular metabolism." [GO:0006744, KEGG:map00130, OneLook:www.onelook.com, PMID:14757233]
synonym: "KEGG:00130" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000143
name: insulin signaling pathway
def: "Processes regulated by insulin and insulin-like growth factor signaling systems include growth and survival of many tissues; for example, neuron and retina, bone, pancreatic beta-cells. Insulin signaling plays important roles in glucose and energy homeostasis. Deregulation of the systems is implicated in a number of metabolic disorders." [GO:0008286, KEGG:map4910, PMID:12169433, Reactome:REACT_498.5]
synonym: "KEGG:04910" RELATED []
synonym: "PID:200014" RELATED []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
relationship: part_of PW:0000357 ! energy homeostasis pathway
relationship: part_of PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000144
name: ubiquitin/proteasome degradation pathway
def: "The pathway for the ATP-dependent non-lysosomal proteolysis catalyzed by the 26S proteasome and for which ubiquitylation, the post-translational covalent conjugation of ubiquitin to target proteins is a key signal." [GO:0006511, KEGG:ko04120, PubMed:2001\, v.27\, 171-179.]
synonym: "KEGG:03050" RELATED []
synonym: "KEGG:04120" RELATED []
is_a: PW:0000417 ! ubiquitin, ubiquitin-like/proteasome degradation pathway

[Term]
id: PW:0000145
name: Metabolism of complex carbohydrates
def: "OBSOLETE. Originally found at KEGG, the term has since been deleted" [PW dictionary:InHouse dictionary]
is_obsolete: true

[Term]
id: PW:0000146
name: glycan metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycans. Glycans are a class of compounds that include oligo- and polysaccharides, simple sugars or polymeric structures of mono- or di-saccharides, respectively. The term also refers to the carbohydrate moiety of glycoproteins, proteoglycans and glycolipids." [OneLook:www.onelook.com]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000147
name: metabolic pathway of secondary metabolites
def: "Those reactions involved in the synthesis, utilization and/or degradation of secondary metabolites - products of cellular metabolism that are not essential for, or not directly involved in the normal growth, development or reproduction of an organism. Many of the chemicals that plants or microorganisms produce are secondary metabolites." [OneLook:www.onelook.com]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000148
name: alkaloid biosynthetic pathway I
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000149
name: alkaloid biosynthetic pathway II
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000150
name: stilbene, coumarine and lignin biosynthetic pathway
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000151
name: starch and sucrose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of starch and sucrose, as depicted in the KEGG diagram. Starch is a polysaccharide produced by all green plants and is an important carbohydrate in the human diet. Sucrose, or the table sugar is a disaccharide of glucose and fructose that is produced by plants and cyanobacteria." [KEGG:map00500, OneLook:http\://www.onelook.com]
synonym: "KEGG:00500" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000152
name: amino sugar metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of amino sugars. An amino sugar has an amino group substituent in place of a hydroxyl group. Amino sugars are important constituents of a variety of polysaccharides and glycoproteins." [GO:0006040, KEGG:map00520, OneLook:www.onelook.com]
comment: Based on Dorland's Medical dictionary
synonym: "KEGG:00520" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000153
name: triacylglycerol metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of triacylglycerols - esters of glycerols with three fatty acid molecules. Triglycerides are the common form of transport and storage of fatty acids. Esters with one or two fatty acid molecules are metabolic intermediates present in small amounts." [GO:0006641, KEGG:map00561, MCW library:QU4 M235b 2009, OneLook:www.onelook.com]
synonym: "triglyceride metabolic pathway" RELATED []
is_a: PW:0001156 ! glycerolipid metabolic pathway

[Term]
id: PW:0000154
name: inositol phosphate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of inositol phosphate which represents all of the possible phosphorylated states of inositol. Inositol phosphates have many important cellular functions." [GO:0043647, KEGG:map00562, OneLook:www.onelook.com]
synonym: "KEGG:00562" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000155
name: phospholipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of phospholipids - lipids containing phosphorus, including those with a glycerol backbone or a backbone of sphingosine or related substances. Phospholipids are the major form of lipid in the cell membrane." [OneLook:www.onelook.com]
is_obsolete: true

[Term]
id: PW:0000156
name: prostaglandin metabolic pathway
def: "Those metabolic reactions involving prostaglandins - a family of prostanoid eicosanoids with many regulatory functions." [MCW library:QU4 M235b 2009]
is_a: PW:0000461 ! cyclooxygenase mediated pathway of arachidonic acid metabolism
is_a: PW:0001240 ! prostanoid metabolic pathway

[Term]
id: PW:0000157
name: glycosaminoglycan metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or  degradation of glycosaminoglycans - any of several high molecular weight linear polysaccharides of repeating disaccharide units. They are important components of connective tissue. When aggregating with proteins, they form proteoglycans." [GO:0030203, MCW Libraries:QU4 V876f 2008, OneLook:www.onelook.com]
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000158
name: Ras family mediated signaling pathway
def: "The Ras family mediated signaling pathways are primarily involved in the regulation of gene expression." [PMID:11152757, PMID:11467446]
is_a: PW:0000006 ! Ras superfamily mediated signaling pathway

[Term]
id: PW:0000159
name: Rab family mediated signaling pathway
def: "Rab family mediated signaling pathways are involved in the regulation of intracellular vesicle trafficking. More than 60 Rab members bind to specific effectors to regulate all aspects of vesicular trafficking - from formation and transport of vesicles, to tethering and fusion with target membranes. Of note is that cytoskeletal rearrangements such as actin remodeling, a process regulated by Rho family, have a role to play in vesicular trafficking." [GO:0032482, PMID:11152757, PMID:16882731, PMID:18171430]
is_a: PW:0000006 ! Ras superfamily mediated signaling pathway

[Term]
id: PW:0000160
name: Ran family mediated signaling pathway
def: "Ran family mediated signaling pathways are involved in nucleocytoplasmic trafficking." [GO:0031291, PMID:11152757]
is_a: PW:0000006 ! Ras superfamily mediated signaling pathway

[Term]
id: PW:0000161
name: glycosylphosphatidylinositol anchor biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of glycosylphosphatidylinositol (GPI) anchor. The GPI anchor allows for the attachment of cell surface proteins to the cell membrane." [GO:0006506, InHouse:InHouse PW dictionary, KEGG:map00563]
synonym: "GPI anchor biosynthesis" RELATED []
synonym: "KEGG:00563" RELATED []
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000162
name: sphingolipid biosynthetic pathway
is_a: PW:0000197 ! sphingolipid metabolic pathway

[Term]
id: PW:0000163
name: sphingolipid degradation pathway
is_a: PW:0000197 ! sphingolipid metabolic pathway

[Term]
id: PW:0000164
name: ganglioside metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of ganglioside - any of a group of glycosphingolipids in which the polar head group on ceramide is a sialic acid. Their names include letters and numbers where the letters M, D and T indicate the number of sialic acid residues in the molecule - one, two or three, respectively." [GO:0001573, OneLook:www.onelook.com]
synonym: "KEGG:00604" RELATED []
is_a: PW:0000733 ! glycosphingolipid metabolic pathway

[Term]
id: PW:0000165
name: taurine and hypotaurine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of taurine and hypotaurine." [InHouse:PW InHouse dictionary, KEGG:map00430]
synonym: "KEGG:00430" RELATED []
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000166
name: monoterpenoid biosynthetic pathway
alt_id: PW:0000252
def: "Those metabolic reactions involved in the synthesis of monoterpenoid. Terpenoids are a large class of naturally-occurring organic chemicals. They are derived from five-carbon units and are modifed in manifold ways." []
synonym: "KEGG:00760" RELATED []
synonym: "monoterpenoid biosynthetic pathway" EXACT []
is_a: PW:0000184 ! terpenoid biosynthetic pathway

[Term]
id: PW:0000167
name: pantothenic acid metabolic pathway
def: "Those metabolic reactions involving pantothenic acid or panthotenate, also known as vitamin B5 - a water-soluble vitamin. Vitamin B5 is the precursor to coenzyme A (CoA) which in turn, plays an essential role in fatty acids and pyruvate metabolism." [KEGG:map00770, OneLook:www.onelook.com]
synonym: "KEGG:00770" RELATED []
synonym: "vitamin B5 metabolic pathway" EXACT []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000168
name: growth factor signaling pathway
def: "Those pathways that are triggered through the binding of a growth factor to its particular receptor. Growth factors carry out mitogenic signaling via their largely tyrosine kinase receptors." [InHouse:PW dictionary, OneLook:www.onelook.com, PMID:16632420]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000169
name: nerve growth factor signaling pathway
def: "Nerve growth factor (NGF) signaling pathways control a variety of processes such as neuronal cell differentiation, axon growth. Members of the NGF family are best known for their anti-apoptotic role as mediators of neuronal cell survival." [GO:0048011, PubMed:Neuron\, 2004\, v42\, p897-912; Cellular Signaling\, 2004\, v16\, p127-36., Reactome:REACT_11061.4]
synonym: "NGF signaling pathway" EXACT []
is_a: PW:0000571 ! neurotrophic factor signaling pathway

[Term]
id: PW:0000170
name: epidermal growth factor/neuregulin signaling pathway
def: "Members of the EGF/neuregulin superfamily are important regulators of tissue development and repair. A characteristic feature is the presence of the EGF module, a 36-40 amino acid sequence with a disulfide-bonded three loop structure necessary for receptor binding." [GO:0007173, KEGG:map04012, MCW e-journal:J. Mol. Evolo.2000\, v50\, p397-412, PubMed:12814936, Reactome:REACT_9417.3]
synonym: "EGF/neuregulin signaling pathway" EXACT []
synonym: "KEGG:04012" RELATED []
synonym: "PID:200101" RELATED []
synonym: "PID:200159" RELATED []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000171
name: disease pathways related to polyQ repeats
def: "A family of neurodegenerative and other inherited diseases that are caused by the expansion of a polyglutamine tract (polyQ) in the associated disease proteins. The diseases are manifested as distinct neuropathies and multiple pathways are perturbed." [PubMed:2004\, v.20(3)\, 146-154]
comment: Definition adapted from an article in Trends in Genetics
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000172
name: spinobulbar muscular atrophy
def: "An inherited neurodegenerative disease caused by an expanded polyQ tract. Various pathways are disrupted and contribute to the manifestation of the condition." [PubMed:2004\, v. 20(3)\, 146-154.]
synonym: "SBMA" RELATED []
is_a: PW:0000173 ! spinocerebellar ataxia

[Term]
id: PW:0000173
name: spinocerebellar ataxia
def: "An inherited form of neurodegenerative disease caused by an expanded polyQ tract. Several types are grouped under SCA, types 1-3, 6, 7 and 17.Various pathways are disrupted and contribute to the manifestation of the condition." [PubMed:2004\, v.20(3)\, 146-154.]
synonym: "SCA" RELATED []
is_a: PW:0000171 ! disease pathways related to polyQ repeats

[Term]
id: PW:0000174
name: metabolic syndrome pathway
def: "The metabolic syndrome is a multiphenotypic condition with concurrent features of several diseases and metabolic abnormalities. Insulin resistance, obesity and hypertension are considered risk factors. Alterations in lipid, glucose and cholesterol metabolic pathways among others, can contribute to the multifactorial metabolic syndrome and the conditions associated with it." [PMID:16932765, PubMed:2004\, v. 17\, 38047]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000175
name: familial combined hyperlipidemia pathway
def: "A possible subset of the metabolic syndrome, characterized  by features such as hypertriglyceridemia, age-dependent changes in plasma total cholesterol, overproduction of triglyceride-rich lipoproteins. Several metabolic and possibly other pathways deviate from their normal functioning." [PubMed :2004\, v.17\, 38-47.]
synonym: "FCHL" RELATED []
relationship: part_of PW:0000174 ! metabolic syndrome pathway

[Term]
id: PW:0000176
name: diabetes pathway
def: "A broad condition with various manifestations that is associated with disruptions of several pathways, primarily those involving insulin signaling. High glucose-mediated oxidative stress on VEGF over-expression and VEGF-mediated signaling are thought to play a role in diabetic retinopathy." [InHouse:PW dictionary, Reactome:REACT_15380.1]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000177
name: diabetic nephropathy pathway
def: "A common complication of diabetes and a leading cause of end stage renal diseases affecting a number of pathways, particularly the thiol and anti-oxidant pathways." [InPress:Manuscript]
is_a: PW:0000176 ! diabetes pathway
is_a: PW:0000300 ! renal system disease, renal disorder pathway

[Term]
id: PW:0000178
name: neurological disorder disease pathway
def: "Neurological disorders are a group of disorders that involve the central nervous system (brain, brainstem and cerebellum), the peripheral nervous system (including cranial nerves), and the autonomic nervous system (parts of which are located in both central and peripheral nervous system). Major branches are headache, stupor and coma, dementia, seizure, sleep disorders, trauma, infections, neoplasms, neuro-ophthalmology, movement disorders, demyelinating diseases, spinal cord disorders, and disorders of peripheral nerves, muscle and neuromuscular junctions. Many mental illnesses are believed to be neurological disorders of the central nervous system, but they are classified separately. They are not traditionally listed as neurological diseases because their causes are not definitely determined as biological, although there are good reasons to suspect that bipolar disorder and schizophrenia have neuro-chemical causes." [OneLook:www.onelook.com]
is_a: PW:0001412 ! nervous system disease pathway

[Term]
id: PW:0000179
name: tuberous sclerosis complex disease pathway
def: "An autosomal dominant condition that often leads to seizure and other neurological symptoms and that may be linked to deregulations in the mTOR signaling pathway." [PubMed:2004\, v.29(1)\, 32-38.]
synonym: "TSC" RELATED []
is_a: PW:0000178 ! neurological disorder disease pathway

[Term]
id: PW:0000180
name: mTOR signaling pathway
def: "mTOR signaling pathway regulates cellular processes such as translation, ribosome biogenesis, cell growth and autophagy and is regulated or responds to growth factors, energy metabolites and/or levels of nutrients." [KEGG:map04150, PubMed:TIBS\, 2004\, v. 29(1)\, 32-38., Reactome:REACT_6838.1]
synonym: "KEGG:04150" RELATED []
synonym: "PID:200096" RELATED []
is_a: PW:0000003 ! signaling pathway
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
relationship: part_of PW:0000357 ! energy homeostasis pathway

[Term]
id: PW:0000181
name: pathway pertinent to protein folding, sorting, modification, translocation and degradation
def: "Those pathways that are involved in or mediate how protein fold or are maintained in a particular folding state, are sorted for translocation or degradation, are modified to regulate their function or to target them for degradation and finally, are degraded." [InHouse:InHouse PW dictionary]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000182
name: lysosomes based pathway of protein degradation
def: "A protein degradation pathway that involves proteases residing in lysosomes and exhibiting optimal activity at an acidic pH (e.g., cathepsins)." [PubMed:2003\, v. 285\, f1-f8.]
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000183
name: the proteolytic pathway involving calcium-dependent proteases
def: "A protein degradation pathway that involves calcium-dependent proteases  (e.g., calpains) ," [PubMed:2003\, v. 285\, f1-f8.]
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000184
name: terpenoid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of terpenoids. The terpenoids, sometimes referred to as isoprenoids, are a class of naturally occurring chemicals. Terpenoids are derived from five-carbon isoprene units and are assembled and modified in manifold ways. They are classified according to the number of isoprene units. The mevalonate pathway and the non-mevalonate MEP/DOXP pathway are the two biosynthetic routes. The first can branch into non-sterol and sterol-producing compounds. The second is only found in plants." [GO:0016114, KEGG:map00900, OneLook:www.onelook.com]
synonym: "KEGG:00900" RELATED []
is_a: PW:0001394 ! terpene and terpenoid biosynthetic pathway

[Term]
id: PW:0000185
name: limonene and pinene degradation pathway
def: "Those metabolic reactions involved in the degradation of limonene -  an essential oil, a monocyclic terpene, found in the peel of oranges and lemons, and pinene - a terpene found in turpentine and many essential oils, used as a solvent and in the manufacture of camphor, insecticides, and synthetic pine oil." [KEGG:map00903, OneLook:www.onelook.com]
is_a: PW:0001399 ! terpene degradation pathway

[Term]
id: PW:0000186
name: streptomycin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of streptomycin - the first of the aminoglycoside antibiotics to be isolated, derived from Streptomyces griseus; it is effective against a wide variety of aerobic gram-negative bacilli and some gram-positive bacteria, including mycobacteria. Its use is now limited because of the emergence of resistant strains." [GO:0019872, KEGG:map00521, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000187
name: erythromycin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of erythromycin -   an intermediate spectrum macrolide (a chemical compound characterized by a large lactone ring containing multiple keto and hydroxyl groups) antibiotic, produced by Streptomyces erythreus, effective against most gram-positive and certain gram-negative bacteria, such as Neisseria species and Haemophilus influenzae, and against spirochetes, some rickettsias, and Entamoeba; it is also highly effective against Mycoplasma pneumoniae. It is used especially in patients allergic to penicillin and in those with penicillin-resistant infections and legionnaires' disease; administered orally or topically." [OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000188
name: pentose and glucuronate interconversion pathway
def: "The series or metabolic reactions involved in the interconversions of the monosaccharide pentose and glucuronate, the salts or esters of glucuronic acid, as depicted in the KEGG diagram." [KEGG:http\://www.genome.ad.jp/kegg/pathway/map/map00040.html, KEGG:map00040]
synonym: "KEGG:00040" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000189
name: folate mediated one-carbon metabolic pathway
def: "Folate mediated one-carbon metabolism represents the one-carbon transfer reactions important for de novo purine and thymidylate biosynthesis and for the remethylation of methionine in the methionine cycle and homocysteine metabolism. The methionine cycle also produces the major methyl donor for proteins, nucleic acids, lipids and other small molecules. The folate mediated one-carbon transfer and the folate cycle pathways are part of folate metabolism." [PMID:11001804, PMID:15166809, PMID:15298442]
synonym: "KEGG:00670" RELATED []
relationship: part_of PW:0000140 ! folate metabolic pathway

[Term]
id: PW:0000190
name: porphyrin and chlorophyll metabolic pathway
def: "Those reactions involved in the synthesis, utilization and/or degradation of porphyrin - any of a group of compounds containing the porphyrin structure, four pyrrole rings connected by methine bridges in a cyclic configuration, to which a variety of side chains may be attached - and chlorophyll - any of a group of green magnesium-containing porphyrin derivatives occurring in all photosynthetic organisms." [KEGG:map00860, OneLook:www.onelook.com]
synonym: "KEGG:00860" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000191
name: keratan sulfate biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of keratan sulfate - a glycosaminoglycan found in the cornea, in cartilage, and in the nucleus pulposus and also as the accumulation product in Morquio's syndrome. It consists of repeating disaccharide units in specific linkage, each composed of a sulfated N-acetylglucosamine residue linked to one of galactose, which is usually sulfated. There are two forms, keratan sulfate I and keratan sulfate II, which differ in carbohydrate content and localization; the former occurs in the cornea and the latter in skeletal tissues." [GO:0018146, KEGG:map00533, OneLook:www.onelook.com]
synonym: "KEGG:00533" RELATED []
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway

[Term]
id: PW:0000192
name: N-linked glycan biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of N-linked glycans. A 14 residue sugar is first built on a dolichol carrier and then attached to the amide group of an asparagine of a nascent polypeptide chain. The asparagine is in a specific amino acid sequence. Subsequent processing involves removal as well as addition of various sugars and produces a wide range of N-glycan structures." [KEGG:map00510, MCW Libraries:QU4 V876f 2008]
synonym: "KEGG:00510" RELATED []
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000193
name: N-Glycan degradation pathway
def: "Those metabolic reactions involved in the degradation of N-Glycans. N-Glycans are found attached to the R-group nitrogen of asparagine." [XPW InHouse Dictionary:InHouse Dictionary]
is_obsolete: true

[Term]
id: PW:0000194
name: O-linked glycan biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of O-linked glycans. Sugars are serially added to a fully synthesized polypeptide chain. The initial step involves the transfer of N-acetylgalactosamine to the carboxy group of a serine or threonine. The location of the residue appears to be dictated by structure rather than amino acid signature." [KEGG:map00512, MCW Libraries:QU4 V876f]
synonym: "KEGG:00512" RELATED []
synonym: "KEGG:00514" RELATED []
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000195
name: chondroitin sulfate biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of chondroitin. Chondroitin is a mucopolysaccharide occurring in sulfated form in various animal tissues (as cartilage)." [GO:0030206, KEGG:map00532, OneLook:www.onelook.com]
synonym: "KEGG:00532" RELATED []
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway

[Term]
id: PW:0000196
name: globoside metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of globoside - a glycosphingolipid containing acetylated amino sugars and simple hexoses." [GO:0001575, OneLook:www.onelook.com]
synonym: "KEGG:00603" RELATED []
is_a: PW:0000733 ! glycosphingolipid metabolic pathway

[Term]
id: PW:0000197
name: sphingolipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of sphingolipids - important components of animal and plant membranes. They contain a long chain amino alcohol and a ceramide core. Ceramides are also the precursors of glycolipids, also referred to as glycosphingolipids, which have attached sugar(s)." [GO:0006665, MCW library:QU4 M235b 2009, OneLook:www.onelook.com, PMID:17976918]
synonym: "KEGG:00600" RELATED []
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000198
name: p38 MAPK signaling pathway
def: "A SAPK MAPK pathway that plays an important role in inflammation and may be involved in several forms of cancer." [GO:0051403, KEGG:map04010, PMID:14570565, PMID:15102355, Reactome:REACT_12065.1]
synonym: "PID:200018" RELATED []
is_a: PW:0000312 ! stress-regulated MAPK signaling pathway

[Term]
id: PW:0000199
name: the Wnt/calcium signaling pathway
def: "A Wnt mediated pathway that is involved in the regulation of cell-cell adhesion and motility." [GO:0007223, KEGG:map04310, PMID:10858654, PMID:12573432]
synonym: "the Wnt/Ca(II) pathway" RELATED []
is_a: PW:0000597 ! Wnt signaling, non-canonical pathway

[Term]
id: PW:0000200
name: Wnt signaling, the planar cell polarity pathway
def: "The planar cell polarity (PCP) Wnt signaling pathway plays an essential in morphogenesis through the regulation of tissues patterning." [GO:006071, KEGG:map04310, PMID:12573432, PMID:16765615]
synonym: "PCP Wnt signaling pathway" RELATED []
is_a: PW:0000597 ! Wnt signaling, non-canonical pathway

[Term]
id: PW:0000201
name: Wnt signaling, canonical pathway
def: "Wnt signaling pathway is involved in many developmental processes. In the conventional or canonical Wnt pathway,  beta-catenin is a central component required for the  transcriptional control of Wnt signaling target genes." [GO:0060070, KEGG:map04310, PMID:12573432, PMID:15001769, PMID:18432252, Reactome:REACT_11045.1]
synonym: "beta-catenin dependent Wnt signaling pathway" RELATED []
synonym: "PID:200077" RELATED []
is_a: PW:0000008 ! Wnt signaling pathway

[Term]
id: PW:0000202
name: homologous recombination pathway of double-strand break repair
def: "A specific pathway for repair of double-strand breaks. It is involved in repair of breaks induced by damaging agents or  generated during meiotic recombination." [GO:0000724, KEGG:map03440, PubMed:Cell\, 2004\, v. 117\, p 171-184, Reactome:REACT_1874.1]
synonym: "homology-directed repair pathway" RELATED []
synonym: "HR pathway of double-strand break repair" EXACT []
synonym: "KEGG:03440" RELATED []
is_a: PW:0000663 ! double-strand DNA repair pathway

[Term]
id: PW:0000203
name: non-homologous end joining pathway of double-strand break repair
def: "A specific pathway for repair of double-strand breaks. Possibly constitutive, it is the most important pathways in mammalian cells and plays an important role in mitotically replicating cells." [GO:0006303, KEGG:map03450, PMID:12947387, PubMed:Cell\, 2004\, v. 117\, 171-184., Reactome:REACT_1022.1]
synonym: "KEGG:03450" RELATED []
synonym: "NHEJ pathway of double-strand break repair" EXACT []
is_a: PW:0000663 ! double-strand DNA repair pathway

[Term]
id: PW:0000204
name: Notch signaling pathway
def: "Notch signaling pathway regulates processes involved in early embryonic development. It plays an important role in cell fate determination. Target genes of Notch have been implicated in angiogenesis, somitogenesis, gliogenesis. Deregulation of the Notch signaling pathway underlies a broad spectrum of diseases and clinical conditions." [GO:0007219, KEGG:map04330, PubMed:Several articles in PubMed, Reactome:REACT_299.2]
synonym: "KEGG:04330" RELATED []
synonym: "PID:200015" RELATED []
is_a: PW:0000332 ! cell-cell signaling pathway
is_a: PW:0000650 ! signaling pathway pertinent to development
is_a: PW:0000656 ! glycoprotein signaling pathway

[Term]
id: PW:0000205
name: dentatorubral-pallidoluysian atrophy disease pathway
def: "Dentatorubral-pallidoluysian atrophy (DRPLA) is caused by an expanded trinucleotide repeat in the DRPLA gene. A very rare condition, it can be sporadic or autosomal dominant inherited. Three forms of DRPLA have been clinically classified:  the ataxo-choreoathetoid form, the pseudo-Huntington form, and the myoclonic epilepsy form. " [NCBI:OMIM database]
synonym: "DRPLA" RELATED []
is_a: PW:0000171 ! disease pathways related to polyQ repeats

[Term]
id: PW:0000206
name: transforming growth factor-beta signaling pathway
def: "Transforming growth factor-beta (TGF-beta) signaling pathway regulates numerous cellular processes such as proliferation, differentiation, migration and cell death. The SMAD dependent pathway represents the core signaling cascade mediated by the TGF-beta superfamily. Mutations in TGF - beta family are responsible for a number of human diseases." [GO:0007179, PMID:15130563, PMID:16678165, PubMed:TIBS\, 2004\, v29 (5)\, p265-273, Reactome:REACT_6844.5]
synonym: "TGF- beta signaling pathway - SMAD dependent" EXACT []
is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway

[Term]
id: PW:0000207
name: central obesity with hypertension pathway
relationship: part_of PW:0000174 ! metabolic syndrome pathway

[Term]
id: PW:0000208
name: type 2 diabetes mellitus pathway
def: "Diabetes mellitus is characterized by abnormally high levels of glucose in the blood. Hereditary and environmental factors are likely contributors but the exact mechanisms are not well understood. Type 2 diabetes mellitus, characterized by insulin resistance, involves alterations in insulin secretion and signaling and impaired glucose homeostasis pathways." [KEGG:map04930, OneLook:www.onelook.com]
synonym: "KEGG:04930" RELATED []
synonym: "T2D pathway" EXACT []
synonym: "type II diabetes mellitus pathway" EXACT []
is_a: PW:0000176 ! diabetes pathway
relationship: part_of PW:0000174 ! metabolic syndrome pathway

[Term]
id: PW:0000209
name: Jak-Stat signaling pathway
def: "The Jak-Stat pathway is a main intracellular cascade initiated primarily in response to cytokine and also other ligand signaling. Four Janus kinases (Jak) and seven signal transducers and activators of transcription (Stat) families of proteins mediate the action of almost 40 cytokine receptors, including the receptor for leptin. Combinations between four Jak(s) and seven Stat(s) shape the outcome of ligand triggered signaling through the various receptors." [GO:0007259, KEGG:map04630, MCW library:Handbook of cellular and molecular immunology, PMID:12039028, PMID:14668806, PMID:14737178, PMID:17312100]
synonym: "KEGG:04630" RELATED []
is_a: PW:0000003 ! signaling pathway
is_a: PW:0000818 ! signaling pathway pertinent to immunity
is_a: PW:0001195 ! tyrosine-specific protein kinase mediated signaling pathway

[Term]
id: PW:0000210
name: SMAD dependent signaling pathways
def: "The core intracellular  signaling cascade mediated  by the TGF-beta superfamily. SMAD proteins function by carrying signals from the cell surface to the nucleus. There are eight vertebrate SMAD proteins and they are activated  by two types of  TGF-beta receptors in response to TGF cytokines binding.There are two known SMAD-dependent TGF-beta signaling pathways. SMAP pathways can also be activated via NGF signalign pathways" [PMID:14534577, PMID:15009204, PubMed:Science\, 2002\, v296\, p1564-7]
is_obsolete: true

[Term]
id: PW:0000211
name: biogenic amines and polyamines metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of biogenic amines and polyamines. Important biogenic amines are histamine, serotonin and the catecholamines.  Spermidine and spermine are examples of important polyamines." [GO:0006595, OneLook:www.onelook.com, PMID:12641342, Reactome:REACT_14820.1]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000212
name: choline metabolic pathway
def: "Choline metabolism is important for the synthesis of phosphatidylcholine in mammalian cells. Its oxidation results in the production of betaine, an important methyl donor. In the brain, it is converted to the powerful neurotransmitter acetylcholine." [PMID:18204095]
is_a: PW:0000211 ! biogenic amines and polyamines metabolic pathway

[Term]
id: PW:0000213
name: RNA polymerase IV transcription pathway
def: "RNA polymerase IV transcription pathway is found in plants and is involved in the synthesis of small interfering RNA (siRNA)." [PMID:15692015]
is_a: PW:0001275 ! eukaryotic RNA polymerase transcription pathway

[Term]
id: PW:0000214
name: polyamine metabolic pathway
def: "Polyamines play important roles in cell growth, proliferation and survival. They can be derived from diet as well as via cellular and intestinal flora mediated biosynthesis." [PMID:19603518]
is_a: PW:0000211 ! biogenic amines and polyamines metabolic pathway

[Term]
id: PW:0000215
name: RNA polymerase V transcription pathway
def: "RNA polymerase V transcription pathway operates in plants and plays a role in heterochromatin formation." [PMID:19377477]
is_a: PW:0001275 ! eukaryotic RNA polymerase transcription pathway

[Term]
id: PW:0000216
name: spermine metabolic pathway
def: "Polyamine metabolism plays important roles in a number of cellular processes. Spermidine and spermine are formed in two consecutive reactions carried out by distinct enzymes that employ the decarboxylated form of AdoMet as an aminopropyl donor." [GO:0008215, PMID:19603518]
is_a: PW:0000214 ! polyamine metabolic pathway

[Term]
id: PW:0000217
name: tetrahydrobiopterin metabolic pathway
def: "Tetrahydrobiopterin is a cofactor for amino acid hydroxylases involved in the synthesis of several neurotransmitters. It can be synthesized de novo from guanosine triphosphate (GTP) or recycled via a regeneration pathway." [OneLook:http\://www.onelook.com]
synonym: "BH4 metabolic pathway" EXACT []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000218
name: heme biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of heme - an iron-containing compound where the iron is complexed within a porphyrin heterocyclic ring. There are several kinds of heme depending on the composition of their side chain. Heme serves as a prosthetic group for a number of proteins." [OneLook:www.onelook.com]
is_a: PW:0000221 ! heme metabolic pathway

[Term]
id: PW:0000219
name: nicotinamide adenine dinucleotide biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of nicotinamide adenine dinucleotide (NAD). NAD can be synthesized de novo from tryptophan or from 'salvageable precursors' such as nicotinamide or nicotinic acid, collectively known as vitamin B3 or niacin. NAD can be phosphorylated to NADP. NAD is used extensively in glycolysis and the citric acid cycle of cellular respiration." [OneLook:www.onelook.com, PMID:18429699]
synonym: "NAD biosynthetic pathway" EXACT []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000220
name: pyridine nucleotide biosynthetic pathway
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000221
name: heme metabolic pathway
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000222
name: UDP-N-acetylgalactosamine biosynthetic pathway
is_obsolete: true

[Term]
id: PW:0000223
name: UDP-N-acetylglucosamine biosynthetic pathway
is_obsolete: true

[Term]
id: PW:0000224
name: N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminic acid dissimilation pathway
def: "Those metabolic reactions leading to the decomposition of N-acetylglucosamine - an acetylated amino sugar that is an important moiety of glycoproteins, N-acetylmannosamine - the acetylated derivative of mannosamine, and N-acetylneuraminic acid - the most common form of sialic acid in mammals." [OneLook:www.onelook.com]
is_a: PW:0000152 ! amino sugar metabolic pathway

[Term]
id: PW:0000225
name: citrulline degradation pathway
def: "Those metabolic reactions involving citrulline. Citrulline, not a DNA coded amino acid, is a product in the urea cycle." [GO:0019241, OneLook:www.onelook.com]
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000226
name: putrescine metabolic pathway
def: "Putrescine, spermidine and spermine are the only polyamines synthesized in mammalian cells. Putrescine, derived from L-ornithine, an important component of the urea cycle, is the substrate for the formation of spermidine, in turn the substrate for spermine." [GO:0009445, PMID:19603518]
is_a: PW:0000214 ! polyamine metabolic pathway

[Term]
id: PW:0000227
name: G protein mediated signaling pathway via Galphas family
def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpa/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PMID:12040175, PMID:15747061]
is_a: PW:0000125 ! G protein mediated signaling pathway
relationship: part_of PW:0000528 ! angiotensin II signaling pathway via AT2 receptor
relationship: part_of PW:0000676 ! glucagon signaling pathway
relationship: part_of PW:0000713 ! vasopressin signaling pathway via receptor type 2
relationship: part_of PW:0000794 ! epinephrine signaling pathway via adrenergic receptor beta
relationship: part_of PW:0000797 ! norepinephrine signaling pathway via adrenergic receptor beta
relationship: part_of PW:0000851 ! dopamine signaling pathway via D1 family of receptors
relationship: part_of PW:0001091 ! serotonin signaling pathway via receptors engaging G alphas protein family
relationship: part_of PW:0001135 ! parathyroid hormone signaling pathway

[Term]
id: PW:0000228
name: G protein mediated signaling pathway via Galphai family
def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpha/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PMID:12040175, PMID:15747061]
is_a: PW:0000125 ! G protein mediated signaling pathway
relationship: part_of PW:0000494 ! oxytocin signaling pathway
relationship: part_of PW:0000527 ! angiotensin II signaling pathway via AT1 receptor
relationship: part_of PW:0000528 ! angiotensin II signaling pathway via AT2 receptor
relationship: part_of PW:0000586 ! orexin/hypocretin signaling pathway via orexin/hypocretin receptor 2
relationship: part_of PW:0000793 ! epinephrine signaling pathway via adrenergic receptor alpha 2
relationship: part_of PW:0000796 ! norepinephrine signaling pathway via adrenergic receptor alpha 2
relationship: part_of PW:0000850 ! glutamate signaling pathway via group II or III glutamate receptor
relationship: part_of PW:0000852 ! dopamine signaling pathway via D2 family of receptors
relationship: part_of PW:0000856 ! acetylcholine signaling pathway via muscarinic acetylcholine receptors engaging G alphai protein family
relationship: part_of PW:0001089 ! serotonin signaling pathway via receptors engaging G alphai protein family
relationship: part_of PW:0001141 ! calcium signaling pathway via the calcium-sensing receptor

[Term]
id: PW:0000229
name: G protein mediated signaling pathway via Galphaq family
def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpha/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PMID:12040175, PMID:15747061]
is_a: PW:0000125 ! G protein mediated signaling pathway
relationship: part_of PW:0000494 ! oxytocin signaling pathway
relationship: part_of PW:0000527 ! angiotensin II signaling pathway via AT1 receptor
relationship: part_of PW:0000585 ! orexin/hypocretin signaling pathway via orexin/hypocretin receptor 1
relationship: part_of PW:0000586 ! orexin/hypocretin signaling pathway via orexin/hypocretin receptor 2
relationship: part_of PW:0000712 ! vasopressin signaling pathway via receptor type 1
relationship: part_of PW:0000792 ! epinephrine signaling pathway via adrenergic receptor alpha 1
relationship: part_of PW:0000795 ! norepinephrine signaling pathway via adrenergic receptor alpha 1
relationship: part_of PW:0000849 ! glutamate signaling pathway via group I metabotropic glutamate receptor
relationship: part_of PW:0000855 ! acetylcholine signaling pathway via muscarinic acetylcholine receptors engaging G alphaq protein family
relationship: part_of PW:0001090 ! serotonin signaling pathway via receptors engaging G alphaq protein family
relationship: part_of PW:0001135 ! parathyroid hormone signaling pathway
relationship: part_of PW:0001141 ! calcium signaling pathway via the calcium-sensing receptor

[Term]
id: PW:0000230
name: G protein mediated signaling pathway via Galpha12/Galpha13 family
def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpa/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PMID:12040175, PMID:15747061]
is_a: PW:0000125 ! G protein mediated signaling pathway
relationship: part_of PW:0000527 ! angiotensin II signaling pathway via AT1 receptor

[Term]
id: PW:0000231
name: Rap1 pathways
def: "A very close relative of Ras, Rap1 mediated pathway  appears to control diverse processes such as modulation of growth and differentiation, secretion, integrin linked cell adhesion, morphogenesis." [PubMed:Nature Reviews\, Mol. Cell Biology\, 2001\, v2\, p369-77.]
is_obsolete: true

[Term]
id: PW:0000232
name: phosphatidylinositol 3-kinase-Akt signaling pathway
def: "Phosphatidylinositol 3-kinase-Akt signaling pathway involving PI3K class I enzymes, particularly class IA, controls various processes such as cell growth, proliferation and survival. Class IA enzymes couples to receptor tyrosine kinases or their adaptors; class IB couples to G-protein coupled receptor mainly via Galphai. The Akt family of protein kinases are activated downstream of class I PI3Ks and collectively (Akt1, 2, and 3) phosphorylate more than 70 cytoplasmic and nuclear substrates. Deregulation of the pathway has been linked to various forms of cancer." [PMID:14737178, PMID:15023437, PMID:15143962]
synonym: "KEGG:04151" RELATED []
synonym: "phosphoinositide 3-kinase-Akt signaling pathway" EXACT []
synonym: "PI3K-Akt signaling pathway" EXACT []
synonym: "PID:200197" RELATED []
is_a: PW:0000963 ! phosphatidylinositol 3-kinase class I signaling pathway
is_a: PW:0001194 ! serine/threonine-specific kinase mediated signaling pathway

[Term]
id: PW:0000233
name: tumor necrosis factor mediated signaling pathway
def: "Tumor necrosis factor (Tnf) signaling plays pivotal roles in immunity, cell proliferation, differentiation and apoptosis by activating several pathways. NF-kB is a major pathway activated by Tnf; others include JNK and P38 MAPK. Through receptor associated adapters Tnf elicits apoptosis via the extrinsic pathway. Deregulation of Tnf signaling has been implicated in a great number of human diseases - cerebral malaria, cancer, multiple sclerosis, are a few examples." [GO:0033209, PMID:12040173, PMID:12655295, PMID:20303867, Reactome:REACT_1432.1]
synonym: "PID:200102" RELATED []
synonym: "TNF signaling pathway" RELATED []
synonym: "TNFalpha signaling pathway" RELATED []
is_a: PW:0000106 ! extrinsic apoptotic pathway
is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway
is_a: PW:0000926 ! pro-inflammatory cytokine mediated pathway

[Term]
id: PW:0000234
name: innate immune response pathway
def: "The innate immune response - a universal and ancient form of host defense against infection - is a first line of response to various pathogens and also to damaged cells. It plays a role in stimulating adaptive immunity; molecules generated during innate responses act as second signals that can impact on both the magnitude and the nature of the adaptive response." [GO:0045087, PMID:11861602, PMID:20303867]
is_a: PW:0000023 ! immune response pathway

[Term]
id: PW:0000235
name: adaptive immune response pathway
def: "The adaptive immune response is an evolutionarily newer mechanism that provides great specificity and diversity of antigen recognition, immunological memory and specialized responses. The two types of adaptive immune response pathways are humoral and cellular or cell-mediated." [GO:0002250, MCW library:Handbook on cellular and molecular immunology, PMID:11861602]
is_a: PW:0000023 ! immune response pathway

[Term]
id: PW:0000236
name: tumor necrosis factor superfamily mediated signaling pathway
def: "Members of TNF superfamily mediate autoimmunity and inflammation, cell proliferation, survival and/or apoptosis through a number of signaling mechanisms that involve activation of nuclear factor-kappaB, of caspases and/or of mitogen-activated protein kinases (MAPK). TNF superfamily has been implicated in a wide range of human diseases including tumorigenesis, septic shock, rheumatoid arthritis and other conditions." [PMID:11239407, PMID:11796220, PMID:14555214]
synonym: "TNF superfamily signaling pathways" RELATED []
is_a: PW:0000828 ! cytokine mediated signaling pathway

[Term]
id: PW:0000237
name: stress response pathway
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000238
name: insulin-like growth factor signaling pathway
def: "Processes regulated by insulin and insulin-like growth factor signaling systems include growth and survival of many tissues; for example, neuron and retina, bone, pancreatic beta-cells. Insulin is best known for its role in the regulation of blood glucose. Deregulation of the systems is implicated in a number of metabolic disorders." [GO:0048009, PMID:12169433]
synonym: "PID:200100" RELATED []
is_a: PW:0000168 ! growth factor signaling pathway
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000239
name: type 1 diabetes mellitus pathway
def: "Diabetes mellitus is characterized by abnormally high levels of glucose in the blood. Hereditary and environmental factors are likely contributors but the exact mechanisms are not well understood. Type 1 diabetes mellitus pathway involves alterations in immune response pathways resulting in destruction of the insulin-producing beta cells." [KEGG:map04940, OneLook:www.onelook.com]
synonym: "KEGG:04940" RELATED []
synonym: "type I diabetes mellitus pathway" EXACT []
is_a: PW:0000176 ! diabetes pathway

[Term]
id: PW:0000240
name: neuropsychiatric disease pathway
def: "Neuropsychiatric diseases are mental disorders due to various defects in the working of the nervous system." [wikipedia:http\://en.wikipedia.org/wiki/Neuropsychiatry]
synonym: "mental disorder pathway" RELATED []
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000241
name: schizophrenia pathway
def: "Schizophrenia is a psychiatric diagnosis denoting a persistent, often chronic, mental illness variously affecting behavior, thinking, and emotion. The term schizophrenia comes from the Greek words schizo, (split or divide) and phrenos, (mind) and is best translated as \"shattered mind\"." [OneLook:www.onelook.com]
is_a: PW:0000240 ! neuropsychiatric disease pathway

[Term]
id: PW:0000242
name: bipolar disorder pathway
def: "As categorized by the DSM-IV, bipolar disorder is a form of mood disorder characterized by a variation of mood between a phase of manic or hypomanic elation, hyperactivity and hyper imagination, and a depressive phase of inhibition, slowness to conceive ideas and move, and anxiety or sadness. Together these form what is commonly known as manic depression. Manic depression, with its two principal sub-types, bipolar disorder and major depression, was first clinically described near the end of the 19th century by psychiatrist Emil Kraepelin, who published his account of the disease in his Textbook of Psychiatry. DSM-IV is the Diagnostic and Statistical Manual of Mental Disorders, published by the American Psychiatric Association, is the handbook used most often in diagnosing mental disorders in the United States and other countries." [OneLook:www.onelook.com]
is_a: PW:0000240 ! neuropsychiatric disease pathway

[Term]
id: PW:0000243
name: vascular endothelial growth factor signaling pathway
def: "The VEGF family plays key roles in angiogenesis and lymphangiogenesis. Through their receptors, VEGFs can initiate a diverse and complex network of signaling cascades. Deregulation of VEGFs mediated pathways, mostly through upregulation of VEGFs expression, has been implicated in a number of conditions, primarily cancer." [GO:0048010, KEGG:map04370, OneLook:www.onelook.com, PMID:15544039, PMID:15563310, Reactome:REACT_12529.1]
synonym: "KEGG:04370" RELATED []
synonym: "PID:200109" RELATED []
synonym: "PID:200188" RELATED []
synonym: "VEGF signaling pathways" EXACT []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000244
name: angiotensin II signaling pathway
def: "Angiotensin II signaling pathways play a critical role in the control of cardiovascular and renal homeostasis. Angiotensin II pathway can also contribute to cardiovascular diseases such as hypertension, atherosclerosis and heart failure." [PMID:15638741, PMID:15883759]
is_a: PW:0000245 ! angiotensin signaling pathway

[Term]
id: PW:0000245
name: angiotensin signaling pathway
def: "Angiotensin peptides Ang II, Ang III, Ang IV and Ang (1-7) generated from a single precursor protein - angiotensinogen - regulate an array of physiological and pathophysiological processes." [PMID:12676163, PMID:12676165, PMID:15638741]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
relationship: part_of PW:0000492 ! renin-angiotensin cascade pathway

[Term]
id: PW:0000246
name: Rheb mediated signaling pathway
def: "The Rheb family of proteins plays an essential role in the regulation of cell growth and cell cycle. Rheb could be a mediator of the mTOR signaling pathway. The results have been shown for Drosophila but remained to be established for mammals." [PMID:15240005]
is_a: PW:0000158 ! Ras family mediated signaling pathway

[Term]
id: PW:0000247
name: transforming growth factor-beta Smad independent signaling pathway
def: "TGF-beta can activate signaling cascades others than the Smad mediated ones, including MAPK pathways such as Erk, p38 and JNK. The mechanisms of MAPK pathways activation by TGF-beta are not well understood." [PMID:14534577]
synonym: "TGF-beta Smad independent signaling pathway" RELATED []
is_a: PW:0000206 ! transforming growth factor-beta signaling pathway

[Term]
id: PW:0000248
name: isoprenoid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of isoprenoids or terpenoids - a large class of organic biomolecules. Isoprenoids are precursors of sterols such as cholesterol and its derivative and also of non-sterols molecules many of which are used in the post-translational modification of proteins. Plant isoprenoids are among the most commonly found and have a broad range of uses and applications in plants and beyond." [MCW library:QU4 M235b 2009, PMID:20015036, PMID:21746700, PMID:22442388]
synonym: "terpenoid metabolic pathway" RELATED []
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000249
name: lipopolysaccharide biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of lipopolysaccharides, also known as lipoglycans, found in the outer membrane of Gram-negative bacteria. They are large molecules consisting of a lipid and a polysaccharide joined by a covalent bond. In host cells they act as endotoxins which are recognized by members of the Toll-like receptors to elicit strong immune responses." [GO:0009103, KEGG:map00540, OneLook:www.onelook.com]
synonym: "lipoglycan biosynthetic pathway" RELATED []
synonym: "LPS biosynthetic pathway" RELATED []
is_a: PW:0000876 ! bacterial polysaccharide metabolic pathway

[Term]
id: PW:0000250
name: peptidoglycan biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of peptidoglycan - a high molecular weight polymer that forms the tough, rigid structure of bacterial cell walls. It is made up of three parts: (1) a backbone, composed of alternating N-acetylglucosamine and N-acetylmuramic acid; (2) a set of identical tetrapeptide side-chains attached to N-acetylmuramic acid; and (3) a set of identical peptide cross-bridges. The backbone is the same in all bacterial species; however, the tetrapeptide side-chains and the peptide cross-bridges vary from species to species." [GO:0009252, KEGG:map00550, OneLook:www.onelook.com]
synonym: "murein biosynthetic pathway" RELATED []
is_a: PW:0000876 ! bacterial polysaccharide metabolic pathway

[Term]
id: PW:0000251
name: diterpenoid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of diterpenoid. Terpenoids are a large class of naturally-occurring organic chemicals. They are derived from five-carbon units and are modifed in manifold ways." [GO:0016102, KEGG:map00904, OneLook:www.onelook.com]
synonym: "KEGG:00904" RELATED []
is_a: PW:0000184 ! terpenoid biosynthetic pathway

[Term]
id: PW:0000253
name: indole and ipecac alkaloid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of indole and ipecac. Indole is a heterocyclic compound, obtained from coal tar, and produced by the decomposition of tryptophan in the intestine, being partly responsible for the peculiar odor of the feces. It is also found in cultures of Vibrio cholerae and other bacteria; a color test for its production is used in classifying enteric bacteria. Ipecac is derived from the dried rhizome and roots of Cephaelis ipecacuanha or of C. acuminata. It is a mixture of alkaloids, primarily emetine and cephaelin." [OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000254
name: penicillins and cephalosporins biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of penicillin and cephalosporins. The former is the best known antibiotic which blocks the cross linking reaction in peptidoglycan synthesis, thus destroying the bacterial cell wall. The latter represents a broad class of antibiotics similar to penicillin, both chemically and in mode of action." [KEGG:map00311, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000255
name: beta-Lactam resistance pathway
def: "Those pathways that confer to an organism resistance to the action of beta-lactams - a class of broad spectrum antibiotics that are structurally and pharmacologically related to penicillins and cephalosporins." [KEGG:map00312, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000256
name: polyketides biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of polyketides. Polyketides are a group of secondary metabolites made by microorganisms that possess a broad range of pharmacologically important activities such as antimicrobial, antifungal, antiparasitic and antitumor." [Internet:http\://linux1.nii.res.in/~pksdb/polyketide.html]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000257
name: polyketide sugar biosynthetic pathway
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000258
name: tetracycline biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of tetracycline - any of a group of biosynthetic antibiotics. Some are isolated from certain species of Streptomyces and others are produced semisynthetically." [GO:0043644, KEGG:map00253, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000259
name: clavulanic acid biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of clavulanic acid. Clavulanic acid is a beta-lactam antibiotic produced by a bacterium of the genus Streptomyces (S. clavuligerus) that is a beta-lactamase inhibitor and is usually used in the form of its clavulanate salt of potassium especially in combination with amoxicillin" [GO:0033050, Internet:Google, KEGG:map00331]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000260
name: puromycin biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of puromycin - an antibiotic produced by Streptomyces alboniger, which has been used experimentally as an antineoplastic because of its ability to inhibit protein synthesis; it also has trypanosomicidal and amebicidal activity and was formerly used in the treatment of African trypanosomiasis and amebic dysentery." [GO:0043638, KEGG:map00231, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000261
name: neuronal secretory pathway
def: "The unique morphology of the neuron defies the classical organization of secretory pathways. The neuronal secretory pathway represents the intracellular trafficking route for proteins involved in synaptic transmission and plasticity as well as for lipids necessary for outgrowth and remodeling of the somatodendritic compartment. Neurons possess both somatic and dendritic Golgi compartments." [PMID:15232591]
is_a: PW:0001251 ! regulatory pathway pertinent to the brain
relationship: part_of PW:0000272 ! neuron-to-neuron signaling pathways

[Term]
id: PW:0000262
name: altered metabolic pathway
def: "Those metabolic pathways that deviate from what their normal course should be. Aberrant metabolic pathways, alone or in combination with other pathways, underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse dictionary]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000263
name: altered regulatory pathway
def: "Those regulatory pathways that deviate from what their normal course should be. Aberrant regulatory pathways, alone or in combination with other pathways underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse Dictionary]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000264
name: altered signaling pathway
def: "Those signaling pathways that deviate from what their normal course should be. Aberrant signaling pathways, alone or in combination with other pathways underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse Dictionary]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000265
name: Creutzfeldt-Jakob disease pathway
def: "Creutzfeldt-Jakob disease -  a rare prion disease, associated with a number of different mutations of the prion protein gene, existing in sporadic, familial (as an autosomal dominant), and infectious forms, with onset usually in middle life, and having a wide variety of clinical and pathological features. The most commonly seen are varying degrees of spongiform degeneration of neurons, neuronal loss, gliosis, and amyloid plaque formation, accompanied by rapidly progressive dementia, myoclonus, motor disturbances." [OneLook:www.onelook.com]
synonym: "CJD" RELATED []
is_a: PW:0000019 ! prion diseases pathway

[Term]
id: PW:0000266
name: Gerstmann-Strussler syndrome, Gerstmann-Strussler-Scheinker syndrome pathway
def: "Gerstmann-Strussler syndrome,   Gerstmann-Strussler-Scheinker syndrome - a group of rare prion diseases, of autosomal dominant inheritance but linked to different mutations of the prion protein gene. Common characteristics include cognitive and motor disturbances, the presence of multicentric amyloid plaques in the brain. Its manifestations include cerebellar ataxia and dementia, rigidity, tremor, memory loss and others, depending on the form of the condition." [OneLook:www.onelook.com]
is_a: PW:0000019 ! prion diseases pathway

[Term]
id: PW:0000267
name: fatal familial insomnia pathway
def: "Fatal familial insomnia - an inherited prion disease, transmitted as an autosomal dominant trait, affecting primarily the ventral and dorsomedial nuclei of the thalamus and characterized by progressive insomnia, hallucinations, stupor, and coma ending in death within 6 months to 3 years of onset; autonomic and motor disturbances are also present." [OneLook:www.onelook.com]
is_a: PW:0000019 ! prion diseases pathway

[Term]
id: PW:0000268
name: kuru
def: "Kuru - an infectious form of prion disease with a long incubation period, found only among the Fore and neighboring peoples of New Guinea. It is thought to be associated with ritual cannibalism. Its manifestations include truncal and limb ataxia, tremor, others; ends invariably in death. Amyloid plaques are present in about two thirds of affected individuals." [OneLook:www.onelook.com]
is_a: PW:0000019 ! prion diseases pathway

[Term]
id: PW:0000269
name: protein folding pathway
def: "Those reactions and molecular interactions underlying the folding of a protein into its functional three-dimensional structure. Folding takes place in the cytoplasm and, in the case of secreted proteins, in the endoplasmic reticulum. Proteins are checked (quality control) for proper folding and misfolded proteins are targeted for degradation." [GO:0006457]
is_a: PW:0000181 ! pathway pertinent to protein folding, sorting, modification, translocation and degradation
relationship: part_of PW:0000280 ! secretory pathway

[Term]
id: PW:0000270
name: presynaptic differentiation
is_a: PW:0000261 ! neuronal secretory pathway

[Term]
id: PW:0000271
name: postsynaptic differentiation
is_a: PW:0000261 ! neuronal secretory pathway

[Term]
id: PW:0000272
name: neuron-to-neuron signaling pathways
is_a: PW:0000059 ! signaling pathway pertinent to the brain

[Term]
id: PW:0000273
name: neuron-to-neuron signaling pathway via the electrical synapse
def: "A simpler pathway of neuron-to-neuron signaling involving the direct flow of ionic currents. It is a reciprocal pathway involving membrane-to-membrane apposition known as gap junction." [PubMed:Annu. Rev. Neurosci. 2004\, v27\, p393-418., Reactome:REACT_16881.2]
is_a: PW:0000272 ! neuron-to-neuron signaling pathways

[Term]
id: PW:0000274
name: neuron-to-neuron signaling pathway via the chemical synapse
def: "A neurotransmitter-releasing pathway of neuron-to-neuron communication. It involves fusion of neurotransmitter-filled synaptic vesicles with the plasma membrane, activation of postsynaptic receptors. It also involves recycling and re-release of synaptic vesicles." [PubMed :Annu. Rev. Neursci. 2003\, v26\, 701-28., Reactome:REACT_13477.2]
synonym: "Neurotransmission pathway" RELATED []
is_a: PW:0000272 ! neuron-to-neuron signaling pathways

[Term]
id: PW:0000275
name: cell death pathway
def: "A cell death pathway represents the particular series of events leading to the demise of a whole cell or parts of its contents. It plays an essential role in cellular and tissues homeostasis. Deregulation of cell death can contribute to the development of cancer and neurodegeneration." [PMID:12196263, PMID:18414491, PMID:20211164]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000276
name: non-apoptotic cell death pathway
def: "Non-apoptotic cell death pathway refers collectively to those types of cell death whose functional and/or morphological features are different from the apoptotic cell death." [PMID:12196263, PMID:18414491]
is_a: PW:0000275 ! cell death pathway

[Term]
id: PW:0000277
name: senescence pathway
is_a: PW:0000276 ! non-apoptotic cell death pathway

[Term]
id: PW:0000278
name: autophagy pathway
def: "Autophagic pathway involves the sequestration of misfolded or long-lived proteins and of defective organelles within double membrane vesicles, delivery of the cargo to lysosomes for degradation and recycling." [Onelook:www.onelook.com, PMID:20034776, PMID:20089931, PMID:20211164]
synonym: "KEGG:04140" RELATED []
is_a: PW:0000276 ! non-apoptotic cell death pathway

[Term]
id: PW:0000279
name: necrosis pathway
def: "Necrosis represents the sum of the morphological changes indicative of cell death and caused by the progressive degradative action of enzymes; it may affect groups of cells or part of a structure or an organ. There are many causes of necrosis including injury, infection, cancer, infarction, inflammation, others. There are several distinctive morphologic patterns of necrosis." [Onelook:www.onelook.com]
is_a: PW:0000276 ! non-apoptotic cell death pathway

[Term]
id: PW:0000280
name: secretory pathway
def: "The secretory pathway is the route by which secreted proteins travel from their biosynthesis and folding to their final destination. It involves ER insertion where folding and quality control of folding take place, move to Golgi and trans-Golgi Network (TGN) where sorting and final modifications take place, exit from Golgi and vesicular transport via exocytosis to final destinations." [PMID:17686625, PMID:18216874, PMID:18354421]
is_a: PW:0000181 ! pathway pertinent to protein folding, sorting, modification, translocation and degradation

[Term]
id: PW:0000281
name: endocytosis pathway
def: "The endocytic pathway allows for recycling of cargo delivered via the exocytic route, uptake of nutrients, internalization of receptors but also the engulfing of dying cells or of material foreign to the cell. Endocytosis can be subdivided into four pathways: Four pathways Endocytosis can take place via the clathrin-mediated endocytosis, caveolae-mediated endocytosis, micropinocytosis and phagocytosis." [GO:0006897, PMID:16882731, PMID:16985500, PMID:18354421]
synonym: "KEGG:04144" RELATED []
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000282
name: benzoate degradation pathway
def: "Those enzymatic reactions involved in the degradation of benzoate - a salt of benzoic acid or benzene carboxylic acid, a fungistatic compound widely used as a food preservative." [GO:0043639, InHouse:PW dictionary]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000283
name: altered glycan metabolic pathway
def: "Those metabolic pathways involving glycan that deviate from what their normal course should be. Aberrant glycan metabolic pathways, alone or in combination with other pathways, underlie various diseases." [PMID:15459677]
is_a: PW:0000146 ! glycan metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000284
name: altered glycosaminoglycan pathway
def: "Those metabolic pathways involving glycosaminoglycans that deviate from what their normal course should be. Aberrant glycosaminoglycan pathways, alone or in combination with other pathways underlie various diseases." [PMID:15459677]
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway
is_a: PW:0000283 ! altered glycan metabolic pathway

[Term]
id: PW:0000285
name: altered heparan sulfate pathway
def: "Those metabolic pathways involving heparan sulfate (HS) that deviate from what their normal course should be. Aberrant HS pathways, alone or in combination with other pathways may be involved in diseases. An example is the potential role of HS in Alzheimer's disease." [PMID:14530380]
is_a: PW:0000284 ! altered glycosaminoglycan pathway
is_a: PW:0000524 ! heparan sulfate biosynthetic pathway

[Term]
id: PW:0000286
name: integrin mediated signaling pathway
def: "Integrins signal bi-directionally across the plasma membrane. Inside-out signaling modulates their interaction with ligands to regulate cell adhesion and ECM organization. Ligand binding initiates and shapes many signaling events and links to the cytoskeleton. Via protein clustering and ECM organization integrins synergize with and/or modulate various growth factor pathways. Integrin signaling regulates multiple processes including gene expression, cell proliferation, differentiation and survival." [GO:0007229, KEGG:map04510, PMID:14570568, PMID:15009204, PMID:15276463, Reactome:REACT_13552.1]
is_a: PW:0000648 ! cell adhesion signaling pathway

[Term]
id: PW:0000287
name: altered apoptotic cell death
def: "Those apoptotic pathways that deviate from what their normal course should be. Aberrant pathways of programmed cell death, alone or in combination with other pathways underlie various diseases." [PW:InHouse]
is_a: PW:0000009 ! apoptotic cell death pathway
is_a: PW:0000289 ! altered cell death pathway

[Term]
id: PW:0000288
name: altered intrinsic apoptotic pathway
def: "An intrinsic apoptotic pathway that deviates from what its normal course should be. Aberrant intrinsic apoptotic pathway, alone or in combination with other pathways underlies various diseases." [PW:InHouse]
is_a: PW:0000104 ! intrinsic apoptotic pathway
is_a: PW:0000287 ! altered apoptotic cell death

[Term]
id: PW:0000289
name: altered cell death pathway
def: "Those pathways of cell death that deviate from what their normal course should be. Aberrant pathways of cell death, alone or in combination with other pathways underlie various diseases." [PW:Inhouse]
is_a: PW:0000263 ! altered regulatory pathway
is_a: PW:0000275 ! cell death pathway

[Term]
id: PW:0000290
name: altered pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
def: "Those pathways involved in and/or controlling DNA replication, cell cycle, DNA repair and preservation of genomic integrity, RNA and protein biosynthesis that deviate from what their normal course should be. Such aberrant pathways, alone or in combination with other pathways underlie various diseases." [PW:Inhouse]
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
is_a: PW:0000263 ! altered regulatory pathway

[Term]
id: PW:0000292
name: altered DNA repair pathway
def: "Those pathways of DNA repair that deviate from what their normal course should be. Aberrant pathways of DNA repair, alone or in combination with other pathways underlie various diseases." [PW:InHouse]
is_a: PW:0000099 ! DNA repair pathway
is_a: PW:0000290 ! altered pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis

[Term]
id: PW:0000293
name: altered pathway pertinent to protein folding, sorting, modification, translocation and degradation
def: "Those pathways of protein folding, sorting, modification, translocation and degradation that deviate from what their normal course should be. Aberrant protein pathways, alone or in combination with other pathways underlie various diseases." [PW:InHouse]
is_a: PW:0000181 ! pathway pertinent to protein folding, sorting, modification, translocation and degradation
is_a: PW:0000263 ! altered regulatory pathway

[Term]
id: PW:0000294
name: altered ubiquitin/proteasome degradation pathway
def: "An ubiquitin/proteasome degradation pathway that deviates from what its normal course should be. Aberrations in the pathway have been implicated in a number of diseases. Examples include certain malignancies, disorders of the immune and inflammatory responses and neurodegeneration." [PMID:14556719]
is_a: PW:0000144 ! ubiquitin/proteasome degradation pathway
is_a: PW:0000418 ! altered ubiquitin, ubiquitin-like degradation pathway

[Term]
id: PW:0000295
name: altered integrin mediated signaling pathway
def: "An integrin signaling pathway that deviates from what its normal course should be. Aberrant integrin signaling pathway, alone or in combination with other pathways underlies various diseases. An example is hypertrophic cardiomyopathy that involves integrins and the synergy between integrins and growth factors. Aberrant integrin signaling has also been correlated with tumor progression in several cancers." [PMID:15276463]
is_a: PW:0000286 ! integrin mediated signaling pathway
is_a: PW:0000671 ! altered cell adhesion signaling pathway

[Term]
id: PW:0000296
name: hypertrophic cardiomyopathy pathway
def: "Hypertrophic cardiomyopathy, or HCM, is a disease of the myocardium (the muscle of the heart) in which a portion of the myocardium is thickened. Many physiological and pathological conditions as well as many pathways underlie the hypertrophic response." [KEGG:map05410, OneLook:www.onelook.org, PMID:15276462]
synonym: "HCM pathway" EXACT []
synonym: "KEGG:05410" RELATED []
is_a: PW:0000022 ! cardiomyopathy pathway

[Term]
id: PW:0000297
name: platelet-derived growth factor signaling pathway
def: "PDGF signaling pathway plays an important role in the regulation of cell growth and survival." [GO:0048008, PMID:14515146, Reactome:REACT_16888.1]
synonym: "PDGF signaling pathway" RELATED []
synonym: "PID:200149" RELATED []
synonym: "PID:200162" RELATED []
synonym: "PID:200201" RELATED []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000298
name: altered growth factor signaling pathway
def: "Those growth factor mediated signaling pathways that deviate from what their normal course should be. Aberrant growth factor mediated pathways, alone or in combination with other pathways underlie various diseases." [PW:InHouse3]
is_a: PW:0000168 ! growth factor signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000299
name: myocardial infarction pathway
def: "Myocardial infarction, commonly known as heart attack, is a serious, sudden heart condition characterized by varying degrees of chest pain, weakness, sweating, nausea, and vomiting, sometimes causing loss of consciousness. It occurs when parts of the heart muscle die because they are not supplied with enough blood." [OneLook:www.onelook.org]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000300
name: renal system disease, renal disorder pathway
def: "The congenital and acquired diseases affecting the kidney." [PW:InHouse]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000301
name: renal failure pathway
def: "Renal failure implies the loss of kidney function. It can be acute and rapidly progressing, or chronic with slow progression. Chronic renal failure may involve a number of kidney diseases and end-stage renal failure is the ultimate consequence." [Onelook:www.onelook.com]
is_a: PW:0000300 ! renal system disease, renal disorder pathway

[Term]
id: PW:0000302
name: glomerulonephritis pathway
def: "Glomerulonephritis is accompanied by inflammation of the capillary loops in the glomeruli of the kidney. It occurs in acute, subacute, and chronic forms and may be secondary to hemolytic streptococcal infection. Evidence also supports possible immune or autoimmune mechanisms." [Onelook:www.onelook.org]
is_a: PW:0000300 ! renal system disease, renal disorder pathway

[Term]
id: PW:0000303
name: p53-dependent G1/S DNA damage checkpoint pathway
def: "The p53-dependent pathway of G1 arrest in response to damaged DNA." [InHouse:PW dictionary, Reactome:REACT_85.1]
synonym: "ATM pathway" RELATED PID []
is_a: PW:0000095 ! G1/S DNA damage checkpoint pathway

[Term]
id: PW:0000304
name: p53-independent G1/S DNA damage checkpoint pathway
def: "The p53-independent pathway of G1/S arrest in response to damaged DNA." [InHouse:PW dictionary, Reactome:REACT_1208.1]
is_a: PW:0000095 ! G1/S DNA damage checkpoint pathway

[Term]
id: PW:0000305
name: altered carbohydrate metabolic pathway
def: "Those pathways of carbohydrate metabolism that deviate from what their normal course should be. Aberrant carbohydrate metabolic pathways, alone or in combination with other pathways, underlie various diseases." [InHouse:PW dictionary]
is_a: PW:0000005 ! carbohydrate metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000306
name: altered galactose metabolic pathway
def: "Those pathways of galactose metabolism that deviate from what their normal course should be. An aberrant galactose metabolic pathways, alone or in combination with other pathways underlies various diseases. One example is the involvement of aberrant galactose catabolism in cancer." [InHouse :PW dictionary]
is_a: PW:0000042 ! galactose metabolic pathway
is_a: PW:0000305 ! altered carbohydrate metabolic pathway

[Term]
id: PW:0000307
name: coagulative necrosis pathway
def: "Coagulative necrosis is typically seen in hypoxic environments. Cell outlines remain after cell death and can be observed by light microscopy (e.g. myocardial infarction, infarct of the spleen)." [Onelook:www.onelook.com]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000308
name: liquefactive necrosis pathway
def: "Liquefactive necrosis is associated with cellular destruction and pus formation (e.g. pneumonia)." [onelook:www.onelook.com]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000309
name: caseous necrosis pathway
def: "Caseous necrosis is a mix of coagulative necrosis and liquefactive necrosis (e.g. tuberculosis)." [OneLook:www.onelook.com]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000310
name: fatty necrosis pathway
def: "Fatty necrosis results from the action of lipases on fatty tissues (e.g. acute pancreatitis)." [Onelook:www.onelook.com]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000311
name: fibrinoid necrosis pathway
def: "Fibrinoid necrosis involves the deposition of fibrin and other plasma proteins in the walls of afferent renal arterioles in malignant hypertension, often accompanied by an inflammatory infiltrate within the walls and thrombosis of the vessel lumen. " [Onelook:www.onelook.com]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000312
name: stress-regulated MAPK signaling pathway
def: "MAPK signaling pathways that are responding to stress or injury as well as inflammatory cytokines" [PMID:10209154, PMID:14570565, PMID:17229475, PMID:17306385]
synonym: "SAPK signaling pathway" RELATED []
is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway

[Term]
id: PW:0000313
name: c-Jun N-terminal kinases MAPK signaling pathway
def: "A stress induced MAPK pathway that regulates an array of processes such as gene expression, cell migration, cytoskeletal organization, apoptosis." [GO:0007254, KEGG:map04010, PMID:15102441]
synonym: "JNK signaling pathway" RELATED []
is_a: PW:0000312 ! stress-regulated MAPK signaling pathway

[Term]
id: PW:0000314
name: calcium/calmodulin dependent signaling pathway
def: "Those signaling pathways that are mediated through the binding of calmodulin - a multifunctional calcium transducer - to its target effectors." [PMID:10884684, PMID:14671000]
synonym: "Ca/CaM dependent signaling pathways" RELATED []
is_a: PW:0001140 ! calcium/calcium-mediated signaling pathway

[Term]
id: PW:0000315
name: calcineurin signaling pathway
def: "Calcineurin - a calcium/calmodulin dependent serine/threonine phosphatase - plays important regulatory roles in cardiac muscle growth and differentiation, memory processes and apoptosis." [PMID:15232210]
is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway
is_a: PW:0000653 ! serine/threonine-specific phosphatase mediated signaling pathway

[Term]
id: PW:0000316
name: calcium/calmodulin dependent kinase signaling pathway
def: "The multifunctional calcium/calmodulin dependent serine/threonine kinases (CAMKs) play important regulatory roles in the cardiac, muscle, nervous and immune tissues. They are represented by CAMK2 whose Ca2+/CaM binding leads to autophosphorylation and activation and the CAMK cascades that depend on an upstream CAMK kinase (CAMKK) for phosphorylation of an \"activation loop\" and subsequent activation. CAMK1 and CAMK4 are the two CAMK signaling cascades." [PMID:21529938]
synonym: "CaMK signaling pathway" RELATED []
is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway
is_a: PW:0001194 ! serine/threonine-specific kinase mediated signaling pathway

[Term]
id: PW:0000317
name: nuclear factor of activated T-cells signaling pathway
def: "Members of the NFAT family of transcription factors, once de-phosphorylated by calcineurin translocate from the cytoplasm to the nucleus where they induce the transcription of genes involved in the immune response, cell-cell interactions. NFAT signaling is believed to play important roles in the development and function of the cardiovascular system." [GO:0033173, PMID:11983154, PMID:12975316]
synonym: "NFAT signaling pathway" RELATED []
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000318
name: altered calcium/calmodulin dependent signaling pathway
def: "Those calcium/CaM dependent pathways that deviate from what their normal course should be. Aberrant calcium/CaM dependent pathways, alone or in combination with other pathways underlie many diseases. One example is the potential role disruptions within these pathways play in cardiac hypertrophy." [PW dictionary:InHouse PW]
synonym: "altered Ca/CaM dependent pathway" RELATED []
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway

[Term]
id: PW:0000319
name: altered calcineurin signaling pathway
def: "A calcineurin signaling pathway that deviates from what its normal course should be. Aberrant calcineurin pathway, alone or in combination with other pathways underlie various diseases. One example is the role a constitutively active calcineurin plays in cardiac hypertrophy, via the NFAT pathway." [PMID:15276472]
is_a: PW:0000315 ! calcineurin signaling pathway
is_a: PW:0000318 ! altered calcium/calmodulin dependent signaling pathway
is_a: PW:0001197 ! altered serine/threonine-specific phosphatase mediated signaling pathway

[Term]
id: PW:0000320
name: novobiocin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of novobiocin, an aminocoumarin antibiotic. It is also known as albamycin or cathomycin and is produced by an actinomycete of the order Actinobacteria." [GO:0043642, KEGG:map00401, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000321
name: altered Hedgehog signaling pathway
def: "A Hedgehog signaling pathway that deviates from what its normal course should be. Aberrant Hedgehog signaling pathway has been involved in a number of human cancers." [PMID:12495844, PMID:15205520]
is_a: PW:0000122 ! Hedgehog signaling pathway
is_a: PW:0000673 ! altered signaling pathway pertinent to development

[Term]
id: PW:0000322
name: ephrin - ephrin receptor bidirectional signaling axis
def: "Ephrins and their receptors constitute a bidirectional signaling pathway transducing forward signals through the receptors and reverse signals through the ephrins that influence the behavior of both interacting cells. The Eph/ephrin axis plays important roles in cell morphology, adhesion and migration. Its disruption has been implicated in several human cancers." [GO:0048013, PMID:15093606]
synonym: "eph/ephrin receptor bidirectional signaling axis" EXACT []
synonym: "PID:200052" RELATED []
synonym: "PID:200059" RELATED []
synonym: "PID:200142" RELATED []
synonym: "PID:200204" RELATED []
synonym: "PID:200216" RELATED []
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000323
name: altered ephrin - ephrin receptor bidirectional signaling pathway
def: "An Eph/ephrin bidirectional axis that deviates from what its normal course should be. Aberrant Eph/ephrins axis has been implicated in a number of human cancers." [PMID:15561600]
is_a: PW:0000322 ! ephrin - ephrin receptor bidirectional signaling axis
is_a: PW:0000336 ! altered cell-cell signaling pathway

[Term]
id: PW:0000324
name: altered Notch signaling pathway
def: "A Notch signaling pathway that deviates from what its normal course should be. Aberrant Notch signaling pathway has been implicated in a number of human cancers." [PMID:11549580, PMID:14988924, PMID:15288257]
is_a: PW:0000204 ! Notch signaling pathway
is_a: PW:0000336 ! altered cell-cell signaling pathway
is_a: PW:0000669 ! altered glycoprotein signaling pathway
is_a: PW:0000673 ! altered signaling pathway pertinent to development

[Term]
id: PW:0000325
name: protein degradation pathway
def: "Those pathways involved in the degradation of proteins." [GO:0030163, InHouse:InHouse PW dictionary]
is_a: PW:0000181 ! pathway pertinent to protein folding, sorting, modification, translocation and degradation

[Term]
id: PW:0000326
name: altered protein degradation pathway
is_a: PW:0000293 ! altered pathway pertinent to protein folding, sorting, modification, translocation and degradation
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000327
name: protein disulphide bond formation pathway
def: "The pathways involved in the formation, reduction and isomerization of disulphide bonds in proteins. Disulphide bonds are essential for the stability of proteins that are secreted or are localized to organelles of the secretory pathway." [PMID:10754564]
is_a: PW:0000269 ! protein folding pathway

[Term]
id: PW:0000328
name: fibroblast growth factor signaling pathway
def: "The family of fibroblast growth factors (FGF) comprises 22 ligands classified into seven phylogenetic subfamilies and three groups by mode of action: the intracellular intracrine and the extracellular paracrine or canonical  and endocrine or hormone-like groups. The paracrine subfamilies signal via the fibroblast growth factor receptors (FGFR), receptor tyrosine kinases (RTK). The endocrine subfamily is FGFR-dependent but the affinity towards the receptors is low and relies on  Klotho family of transmembrane proteins. The intracrine subfamily is FGFR-independent. Overall, the pathway plays important roles during embryonic and postnatal development, neuromodulation, mineral metabolism and homeostasis. Deregulation of the pathway has been associated with neoplastic and metabolic diseases." [GO:0007173, PMID:19379279, PMID:19601767, PMID:20940169, PMID:22298654, Reactome:REACT_9470.2]
synonym: "FGF signaling pathway" RELATED []
synonym: "PID:200220" RELATED []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000329
name: transforming growth factor-beta superfamily mediated signaling pathway
def: "The TGF-beta superfamily of growth factors regulates a broad spectrum of processes such as angiogenesis, embryonic development, cell differentiation, proliferation, wound healing. Binding to two types of serine/threonine receptors and activation of Smad proteins is a common theme. However, ligand-receptor interaction and the identity of the activated Smad protein(s) appear to be member specific." [KEGG:map04350, PMID:15473857]
synonym: "KEGG:04350" RELATED []
synonym: "TGF-beta superfamily mediated signaling pathway" EXACT []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000330
name: Bone morphogenetic proteins signaling pathway
def: "The bone morphogenetic proteins (BMP) are related to TGF-beta and activins and are members of the TGF-beta superfamily. The BMP signaling pathway plays important roles in induction and patterning of the mesoderm. BMP pathway cross-talks to other pathways such as TGF-beta, Wnt, MAPK, Notch, JAK-STAT and others." [GO:0030509, PMID:15368350, Reactome:REACT_12034.1]
synonym: "BMP signaling pathway " EXACT []
synonym: "PID:200144" RELATED []
is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway
is_a: PW:0000650 ! signaling pathway pertinent to development

[Term]
id: PW:0000331
name: activin signaling pathway
def: "Activins are members of the TGF-beta superfamily of growth factors. The pathway plays important roles in embryonic development, inflammation, reproductive biology. Deregulation of activin signaling contributes to a number of pathological conditions." [GO:0032924, PMID:16885529, PMID:16997617, PMID:19273500]
synonym: "PID:200029" RELATED []
is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway

[Term]
id: PW:0000332
name: cell-cell signaling pathway
def: "Cell-cell signaling pathway conveys information between cells using cell adhesion molecules." [RGD:InHouse dictionary]
is_a: PW:0000648 ! cell adhesion signaling pathway

[Term]
id: PW:0000333
name: cadherin mediated signaling pathway
def: "Cadherins represent a large protein superfamily with many and important roles in cell adhesion and signaling. Cadherins are characterized by the presence of the extracellular cadherin, calcium-binding repeat. The number and structural similarities of repeats across families vary." [PMID:11171368, PMID:18848899]
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000334
name: connexin signaling pathway
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000335
name: altered transforming growth factor-beta superfamily mediated signaling pathway
def: "Those TGF-beta superfamily mediated signaling pathways that deviate from what their normal course should be. Alone or in combination with other pathways they underlie many conditions such as pulmonary hypertension and various types of cancer." [PMID:18313409]
synonym: "altered TGF-beta superfamily mediated signaling pathway" RELATED []
is_a: PW:0000298 ! altered growth factor signaling pathway
is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway

[Term]
id: PW:0000336
name: altered cell-cell signaling pathway
def: "Those cell-cell signaling pathways that deviate from what their normal course should be." [PW dictionary:InHouse PW dictionary]
is_a: PW:0000332 ! cell-cell signaling pathway
is_a: PW:0000671 ! altered cell adhesion signaling pathway

[Term]
id: PW:0000337
name: selectin signaling pathway
def: "Selectins represent a small family of lectin-like adhesion receptors that mediate cell-cell interactions via calcium-dependent recognition of sialylated glycans. The exact role of this signaling pathway is not well known." []
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000338
name: altered cadherins mediated signaling pathway
is_a: PW:0000333 ! cadherin mediated signaling pathway

[Term]
id: PW:0000339
name: altered connexins mediated signaling pathway
is_a: PW:0000334 ! connexin signaling pathway

[Term]
id: PW:0000340
name: altered Notch signaling pathway involving the main players
def: "An altered Notch signaling pathway due to mutation(s) in the main players. They include receptor(s), ligand(s), and members of the CSL complex." [InHouse:PW dictionary]
is_a: PW:0000324 ! altered Notch signaling pathway

[Term]
id: PW:0000341
name: altered Notch signaling pathway involving the macromolecules modifying the main players
def: "An altered Notch signaling pathway due to mutation(s) in the enzymes, macromolecules that act upon the main players. They include proteases, elements of the proteo- and glucosaminoglycan metabolic pathways, ubiquitin ligases, other proteins that modulate availability, sensitivity, endocytosis of ligands/receptors." [InHouse:PW dictionary]
is_a: PW:0000324 ! altered Notch signaling pathway

[Term]
id: PW:0000342
name: altered Notch signaling pathway involving target gene(s)
def: "An altered Notch signaling pathway due to mutation(s) in the target gene(s). They may include members of the HES and HERP families of basic helix-loop-helix (bHLH) transcriptional repressors." [InHouse:PW dictionary]
is_a: PW:0000324 ! altered Notch signaling pathway

[Term]
id: PW:0000343
name: altered Notch signaling pathway involving promoters
def: "An altered Notch signaling pathway due to mutation(s) in the promoters of target gene(s)." [InHouse:PW dictionary]
is_a: PW:0000324 ! altered Notch signaling pathway

[Term]
id: PW:0000344
name: cerebrovascular disease pathway
is_a: PW:0001412 ! nervous system disease pathway

[Term]
id: PW:0000345
name: cerebral arterial diseases pathway
is_a: PW:0000344 ! cerebrovascular disease pathway

[Term]
id: PW:0000346
name: CADASIL pathway
def: "CADASIL - cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy - a disease of the small cerebral arteries characterized by subcortical stroke and vascular dementia. It is associated with mutations in the Notch3 gene. More than fifty mutations are clustered within the first EGF repeats and involve the gain or loss of a cysteine." [PMID:14667809, PMID:14986825]
is_a: PW:0000345 ! cerebral arterial diseases pathway

[Term]
id: PW:0000347
name: cardiovascular abnormalities pathway
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000348
name: congenital heart defects pathway
is_a: PW:0000347 ! cardiovascular abnormalities pathway

[Term]
id: PW:0000349
name: Alagille syndrome pathway
def: "Alagille syndrome is a developmental disease characterized by defects in heart, as well as liver, skeleton and eye. Abnormalities of the central nervous system are also found. The disease is associated with mutations across the entire Jag1 gene." [PMID:14986825]
is_a: PW:0000348 ! congenital heart defects pathway

[Term]
id: PW:0000350
name: altered vascular endothelial growth factor signaling pathway
def: "A VEGF mediated pathway that deviates from what its normal course should be. Aberrant VEGF mediated pathways have been implicated in a number of human cancers. Upregulation of VEGF expression is associated with cancer and tumor growth." [PMID:15563310]
synonym: "altered VEGF signaling pathways" RELATED []
is_a: PW:0000243 ! vascular endothelial growth factor signaling pathway
is_a: PW:0000298 ! altered growth factor signaling pathway

[Term]
id: PW:0000351
name: altered vascular endothelial growth factor signaling pathway involving the main players
def: "An altered VEGF signaling pathway due to mutation(s) in the main players. They include the various VEGF molecules and VEGF receptors." [InHouse:InHouse PW dictionary]
synonym: "altered VEGF signaling pathway involving the main players" RELATED []
is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway

[Term]
id: PW:0000352
name: altered vascular endothelial growth factor signaling pathway involving the macromolecules modifying the main players
def: "An altered VEGF signaling pathway due to mutation(s) in the enzymes that process VEGF, such as the plasmin and furin-like proteases." [InHouse:In House PW dictionary]
synonym: "altered VEGF signaling pathway involving the macromolecules modifying the main players" RELATED []
is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway

[Term]
id: PW:0000353
name: altered vascular endothelial growth factor signaling pathway involving proteins affecting its expression
def: "An altered VEGF signaling pathway due to mutation(s), any activity change in the proteins that regulate VEGF expression. They include transcription factors such as the hypoxia-inducible factor and the many proteins impacting on the stability and/or activity of these factors." [InHouse :InHouse PW dictionary]
synonym: "altered VEGF signaling pathway involving proteins affecting its expression" RELATED []
is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway

[Term]
id: PW:0000354
name: glycerophospholipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycerophospholipids, also known as phospholipids. They are key components of membranes and some are also involved in signaling." [GO:0006650, KEGG:map00564, MCW library:QU4 M235b 2009]
synonym: "KEGG:00564" RELATED []
synonym: "phospholipid metabolic pathway" RELATED []
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000355
name: homeostasis pathway
def: "Those pathways involved in the maintenance of the internal environment of an organism, the adequate levels of substances and nutrients, the stability of normal body states and the feedback regulatory mechanisms that control them." [OneLook:www.onelook.com]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000356
name: oxygen homeostasis pathway
def: "The pathways involved in responding to changes in and maintenance of adequate oxygen levels." [GO:0032364, PMID:11181957, PMID:12603312, PMID:14597660, PMID:15031665]
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000357
name: energy homeostasis pathway
def: "Those pathways involved in the balance between energy uptake and energy expenditure. Disturbance of this equilibrium has been linked to various conditions including obesity." [PMID:11239410, PMID:15703762]
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000358
name: altered homeostasis pathway
def: "Those homeostatic pathways that deviate from what their normal course should be. Aberrant homeostatic pathways, alone or in combination with other pathways, underlie many conditions, disorders and/or diseases." [PW dictionary:PW InHouse dictionary]
is_a: PW:0000263 ! altered regulatory pathway
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000359
name: altered energy homeostasis pathway
def: "Those pathways of energy homeostasis that deviate from what their normal course should be. Obesity in particular has been associated with disturbances in the control of energy balance." [PMID:11239410, PMID:15703762]
is_a: PW:0000357 ! energy homeostasis pathway
is_a: PW:0000358 ! altered homeostasis pathway

[Term]
id: PW:0000360
name: hypoxia inducible factor pathway
def: "The hypoxia inducible transcription factor is activated in response to hypoxic conditions to promote the expression of many genes that play important roles in glucose and energy metabolism, angiogenesis and erythropoiesis." [PMID:11181957, PMID:12603312, PMID:14597660, PMID:15031665]
synonym: "HIF pathway" EXACT []
synonym: "PID:200036" RELATED []
synonym: "PID:200202" RELATED []
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
relationship: part_of PW:0000356 ! oxygen homeostasis pathway

[Term]
id: PW:0000361
name: altered oxygen homeostasis pathway
is_a: PW:0000356 ! oxygen homeostasis pathway
is_a: PW:0000358 ! altered homeostasis pathway

[Term]
id: PW:0000362
name: the ion channels pathway
def: "The acute hypoxic response is mediated through the activity of excitable cells via oxygen-sensing ion channels." [PMID:11181957]
relationship: part_of PW:0000356 ! oxygen homeostasis pathway

[Term]
id: PW:0000363
name: leptin system pathway
def: "Leptin acts on two populations of hypothalamic neurons that express orexigenic (feeding inducing) and anorexigenic genes, respectively. Leptin reduces the expression of genes from the former and enhances the expression of genes from the latter neurons. Leptin mediated response acts primarily via Jak-dependent activation of STAT." [GO:0033210, PMID:11239410, PMID:12079865]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
relationship: part_of PW:0000357 ! energy homeostasis pathway

[Term]
id: PW:0000364
name: altered leptin system pathway
is_a: PW:0000359 ! altered energy homeostasis pathway
is_a: PW:0000363 ! leptin system pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway

[Term]
id: PW:0000365
name: melanocortin system pathway
def: "The melanocortin dependent system is involved in a diverse number of pathways such as pigmentation, steroidogenesis, sexual function, energy homeostasis. Its implication in energy homeostasis is of particular interest as alterations of this system have been associated with obesity." [PMID:11874690, PMID:12556347, PMID:15189116]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
relationship: part_of PW:0000357 ! energy homeostasis pathway

[Term]
id: PW:0000366
name: altered melanocortin system pathway
def: "A melanocortin dependent system pathway that deviates from what its normal course should be. Mutations in the prohormone gene PMOC and the modifying enzyme PC1 are linked to obesity. Mutations in MC2R receptor and its accessory protein MRAP have been associated with type 1 and 2 familial glucocorticoid deficiency, respectively." [PMID:11874690, PMID:19028547]
is_a: PW:0000359 ! altered energy homeostasis pathway
is_a: PW:0000365 ! melanocortin system pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway

[Term]
id: PW:0000367
name: altered Jak-Stat signaling pathway
def: "Jak-Stat signaling pathways that deviate from what their normal course should be." [InHouse:PW InHouse dictionary]
is_a: PW:0000209 ! Jak-Stat signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000368
name: Non-Stat, Jak dependent pathway
def: "Those pathways dependent on activation by JAK kinases but independent of Stat proteins." [PMID:12884916]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000369
name: nuclear factor, erythroid derived 2, like 2 signaling pathway
def: "The nuclear factor, erythroid derived 2, like  (Nfe2l2) also known as Nrf2 is a redox sensitive transcription factor that regulates the expression of phase II drug- and xenobiotic- metabolizing enzymes and of other antioxidant as well as anti-inflammatory genes." [PMID:15252150, PMID:20486759, PMID:20815789, PMID:22874821]
synonym: "Nrf2 signaling pathway" EXACT []
is_a: PW:0000124 ! cellular detoxification pathway
is_a: PW:0000378 ! oxidative stress response pathways
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001229 ! xenobiotic metabolic pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000370
name: aryl hydrocarbon receptor signaling pathway
def: "The aryl hydrocarbon receptor (AhR) is a transcription factor whose ligands include a variety of aromatic hydrocarbons and which regulates the expression of phase I and phase II drug- and xenobiotic-metabolizing enzymes. Phase I enzymes convert otherwise inactive hydrocarbons into active metabolites with potential carcinogenic effects, thus rendering AhR a player in tumor initiation." [PMID:15451023, PMID:15627472, PMID:20106901, PMID:20868221]
synonym: "AhR signaling pathway" EXACT []
is_a: PW:0000124 ! cellular detoxification pathway
is_a: PW:0001229 ! xenobiotic metabolic pathway
is_a: PW:0001371 ! basic helix-loop-helix signaling pathway

[Term]
id: PW:0000371
name: calcium homeostasis pathway
def: "The maintenance of adequate intracellular calcium levels are crucial in order to assure the availability of this important ion and, at the same time prevent against the damage its high concentration can cause. Pumps and exchangers move the calcium ions into organelles or outside the cell, channels of many types allow for its transient flow inside the cell. Calcium transport, which maintains and controls the calcium gradient, and calcium signaling, which the gradient promotes, are inextricably connected in the fabric of calcium homeostasis." [PMID:17574670, PMID:18083096]
is_a: PW:0000589 ! metal homeostasis pathway

[Term]
id: PW:0000372
name: altered calcium homeostasis pathway
def: "Dysfunction of calcium homeostasis has been implicated in several human neural, neurodegenerative and cardiac conditions." [PMID:21170867, PMID:21698698, PMID:22435804]
is_a: PW:0000358 ! altered homeostasis pathway
is_a: PW:0000371 ! calcium homeostasis pathway

[Term]
id: PW:0000373
name: glutathione conjugation pathway
def: "The glutathione conjugation of endogenous and exogenous electrophilic compounds represents a major pathway phase II biotransformation. The glutathione conjugates may either be excreted or undergo further processing." [MCW - book:QV 600 C335t 2001, PMID:17482904, Reactome:REACT_6959.3]
synonym: "phase II biotransformation" RELATED []
is_a: PW:0000378 ! oxidative stress response pathways
is_a: PW:0000858 ! phase II biotransformation pathway

[Term]
id: PW:0000374
name: alternate pathways of glutathione conjugates processing
def: "Pathways of glutathione conjugates processing other than the mercapturic acid pathway." [InHouse dictionary:PW InHouse dictionary]
is_a: PW:0000373 ! glutathione conjugation pathway

[Term]
id: PW:0000375
name: phase I biotransformation pathway via cytochrome P450
def: "The major phase I biotransformation pathway for the activation of endogenous and exogenous substances carried out by members of the cytochrome P450 superfamily." [Book: QV 600 C335t 2001, PMID:17482904, PMID:19835560, Reactome:REACT_13705.1]
synonym: "KEGG:00980" RELATED []
synonym: "KEGG:00982 " RELATED []
is_a: PW:0000857 ! phase I biotransformation pathway

[Term]
id: PW:0000376
name: cytochrome P450-independent phase I biotransformation pathway
def: "A minor phase I biotransformation pathway for the activation of endogenous and exogenous substances carried by flavin-containing monooxygenases." [PMID:19835560]
is_a: PW:0000857 ! phase I biotransformation pathway

[Term]
id: PW:0000377
name: glutathione conjugates processing - the mercapturic acid pathway
def: "The mercapturic acid pathway of glutathione conjugates processing involves the sequential cleavage of glutamyl and glycine residues of glutathione followed by cysteine N-acetylation." [MCW book:QV 600 C335t 2001]
is_a: PW:0000373 ! glutathione conjugation pathway

[Term]
id: PW:0000378
name: oxidative stress response pathways
def: "Oxidative stress occurs when the redox balance between pro- and anti-oxidants is upset due to an increase in endogenous or exogenous pro-oxidant stimuli. The response triggers the upregulation of antioxidant and detoxification systems. Oxidants can also act as second messengers to trigger a variety of cellular signaling pathways." [GO:0006979, InHouse:PW InHouse dictionary]
is_a: PW:0000237 ! stress response pathway

[Term]
id: PW:0000379
name: endoplasmic reticulum stress  - the unfolded protein response pathway
def: "Inhibition of protein folding or its disruption by mutant proteins in the endoplasmic reticulum triggers a signal transduction response known as the unfolded protein response (UPR). UPR increases the biosynthetic capacity while decreasing the biosynthetic burden of the secretory pathway through up- and downregulation of gene expression." [GO:0030968, PMID:15603751, PMID:15952902]
synonym: "ER stress - UPR pathway" RELATED []
is_a: PW:0000237 ! stress response pathway

[Term]
id: PW:0000380
name: transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites
def: "Drugs, endogenous and/or exogenous compounds processed through the phase I and II of  bioactivation, biotransformation pathways are eliminated via phase III transport pathway carried out by several transporter families." [GO:0015893, PMID:17220560]
is_a: PW:0000103 ! transport pathway
is_a: PW:0000124 ! cellular detoxification pathway
is_a: PW:0000378 ! oxidative stress response pathways
is_a: PW:0001229 ! xenobiotic metabolic pathway

[Term]
id: PW:0000381
name: multidrug resistance-associated protein mediated transport pathway
synonym: "MRP mediated pathway" RELATED []
is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites

[Term]
id: PW:0000382
name: multidrug resistance protein mediated transport pathway
synonym: "MDR mediated pathway" RELATED []
is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites

[Term]
id: PW:0000383
name: multispecific organic anion transporter mediated transport pathway
synonym: "OAT mediated pathway" RELATED []
is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites

[Term]
id: PW:0000384
name: G2/M DNA damage checkpoint pathway
def: "The G2M checkpoint pathways assure the genome is replicated only once per cell cycle. The checkpoints control for damaged and un-replicated DNA. Various DNA damage checkpoints lead to inhibition of the cyclin- dependent kinases that regulate the next cell cycle point." [InHouse:PW dictionary, Reactome:REACT_897.2]
is_a: PW:0000096 ! G2/M checkpoint pathway

[Term]
id: PW:0000385
name: G2/M DNA replication checkpoint pathway
def: "Those pathways that assure the genome is replicated only once per cell cycle. The checkpoints control for damaged and un-replicated DNA. Un-replicated DNA signals to block the cell cycle from proceeding. The mechanism by which the cell detects un-replicated DNA is not known." [InHouse:PW dictionary, Reactome:REACT_1846.2]
is_a: PW:0000096 ! G2/M checkpoint pathway

[Term]
id: PW:0000386
name: Rap1 mediated signaling pathway
def: "A very close relative of Ras, Rap1 mediated pathway  appears to control diverse processes such as modulation of growth and differentiation, secretion, integrin linked cell adhesion, morphogenesis." [PMID:11331911]
is_a: PW:0000158 ! Ras family mediated signaling pathway

[Term]
id: PW:0000387
name: Arf family mediated signaling pathway
def: "Arf family mediated signaling pathways are involved in the regulation of intracellular vesicle trafficking. In particular they appear to control early events such as vesicle budding." [GO:0032011, PMID:11152757]
synonym: "PID:200195" RELATED []
is_a: PW:0000006 ! Ras superfamily mediated signaling pathway

[Term]
id: PW:0000388
name: Reelin signaling pathway
def: "Reelin signaling pathway regulates neuronal positioning and may also play a role in synaptic plasticity. The reelin gene appears to be downregulated in the schizophrenic brains but the link between the reelin pathway and the disease remains to be established." [PMID:12764038, PMID:14715136, PMID:14993361]
synonym: "PID:200062" RELATED []
is_a: PW:0000059 ! signaling pathway pertinent to the brain
is_a: PW:0000656 ! glycoprotein signaling pathway

[Term]
id: PW:0000389
name: altered pathway pertinent to signaling in the brain
is_a: PW:0000059 ! signaling pathway pertinent to the brain
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000390
name: altered Reelin signaling pathway
is_a: PW:0000388 ! Reelin signaling pathway
is_a: PW:0000389 ! altered pathway pertinent to signaling in the brain
is_a: PW:0000669 ! altered glycoprotein signaling pathway

[Term]
id: PW:0000391
name: altered Ras superfamily mediated signaling pathway
synonym: "altered monomeric G protein mediated signaling pathway" RELATED []
is_a: PW:0000006 ! Ras superfamily mediated signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000392
name: altered Ras mediated signaling pathway
def: "A Ras mediated signaling pathway that deviates from what its normal course should be. Aberrant Ras mediated signaling pathways have been implicated in a number of human cancers and deregulation of Ras has been reported even in the absence of mutations." [PMID:11027944]
is_a: PW:0000391 ! altered Ras superfamily mediated signaling pathway
is_a: PW:0000525 ! Ras mediated signaling pathway

[Term]
id: PW:0000393
name: altered mTOR signaling pathway
is_a: PW:0000180 ! mTOR signaling pathway
is_a: PW:0000290 ! altered pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
is_a: PW:0000359 ! altered energy homeostasis pathway

[Term]
id: PW:0000394
name: dopamine signaling pathway
def: "Dopamine signaling plays important roles in processes such as motivation, learning and movement. It also plays several roles in the periphery as a modulator of renal and cardiovascular and the endocrine systems. Dopamine signals to a family of at least 5 receptors that are classified into two subfamilies that couple to distinct G proteins to elicit diverse downstream events. Deregulation of the pathway has been implicated in several neuropsychiatric and neurological disorders." [GO:0007212, PMID:17408758, PMID:18353279]
synonym: "dopaminergic pathway" RELATED []
synonym: "KEGG:04728" RELATED []
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse
is_a: PW:0000798 ! catecholamine signaling pathway

[Term]
id: PW:0000395
name: altered dopamine signaling pathway
synonym: "altered dopaminergic pathway" RELATED []
is_a: PW:0000389 ! altered pathway pertinent to signaling in the brain
is_a: PW:0000394 ! dopamine signaling pathway

[Term]
id: PW:0000396
name: spermidine metabolic pathway
def: "Polyamine metabolism plays important roles in a number of cellular processes. Spermidine and spermine are formed in two consecutive reactions carried out by distinct enzymes that employ the decarboxylated form of AdoMet as an aminopropyl donor." [GO:0008216, PMID:19603518]
is_a: PW:0000214 ! polyamine metabolic pathway

[Term]
id: PW:0000397
name: cobalamin metabolic pathway
def: "Those metabolic reactions involving cobalamin, known as vitamin B12 - a water-soluble vitamin. Cobalamin which important roles in a number of metabolic pathways. There are several related compounds whose synthesis occurs in bacteria but whose conversion can be carried out in higher organisms." [OneLook:http\://www.onelook.com]
synonym: "Vitamin B12 metabolic pathway" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000398
name: homocysteine metabolic pathway
def: "Homocysteine (Hcy) metabolism is at the intersection of two pathways: the remethylation pathway that regenerates methionine and thus the methionine cycle and the transsulfuration pathway that gives rise to cysteine and derivatives. Hcy pathway also engages choline, folate, vitamin(s) metabolism and links to the metabolism of other amino acids and compounds." [MCW library book :Homocysteine in Health and Disease - edited by Ralph Carmel and Donald W Jacobsen]
synonym: "Hcy metabolism" RELATED []
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000399
name: remethylation pathway of homocysteine metabolism - cobalamin dependent
relationship: part_of PW:0000398 ! homocysteine metabolic pathway

[Term]
id: PW:0000400
name: transsulfuration pathway of homocysteine metabolism
def: "The transulfuration pathway is one of the two routes of homocysteine metabolism. It allows for the transfer of sulfur from methionine to cysteine. 70% of cysteine is then converted to glutathione and the remainder ends up as either taurine or pyruvate and sulfate." [MCW library book:Homocysteine in Health and Disease - edited by Ralph Carmel and Donald W Jacobsen]
relationship: part_of PW:0000398 ! homocysteine metabolic pathway

[Term]
id: PW:0000401
name: remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent
relationship: part_of PW:0000398 ! homocysteine metabolic pathway

[Term]
id: PW:0000402
name: altered metabolic pathway of other amino acids
def: "Those metabolic pathways of amino acids other than the common amino acids that deviate from what their normal course should be. Aberrant metabolic pathways of other amino acids, alone or in combination with other pathways, underlie various diseases." [InHouse :PW InHouse dictionary]
is_a: PW:0000132 ! metabolic pathway of other amino acids
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000403
name: altered amino acid metabolic pathway
def: "Those pathways of amino acid metabolism that deviate from what their normal course should be. Aberrant amino acid metabolic pathways, alone or in combination with other pathways, underlie various diseases." [InHouse :PW InHouse dictionary]
is_a: PW:0000011 ! amino acid metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000404
name: creatine metabolic pathway
def: "Those metabolic reactions involving creatine. Officially methyl guanidino-acetic acid formed from arginine and glycine and the methyl group of methionine, creatine supplies energy to muscle cells." [GO:0006600, Onelook:www.onelook.com, PMID:10893433, Reactome:REACT_813.2]
is_a: PW:0000033 ! energy metabolic pathway
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000405
name: synaptic vesicle exocytosis - neurotransmitter release pathway
def: "Release of neurotransmitters is mediated through the exocytosis of neurotransmitter-filled synaptic vesicles. Synaptic vesicle trafficking cycle is composed of a number of steps that culminate in calcium-triggered fusion and release." [PMID:10488439, PMID:15217342]
is_a: PW:0001072 ! synaptic vesicle cycle pathway

[Term]
id: PW:0000406
name: metabolic pathway pertinent to the brain
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000407
name: neurotransmitter metabolic pathway
is_a: PW:0000406 ! metabolic pathway pertinent to the brain

[Term]
id: PW:0000408
name: acetylcholine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of acetylcholine - an ester of choline and acetic acid that acts as a neurotransmitter in both the peripheral nervous system and the central nervous system." [OneLook:www.onelook.com]
is_a: PW:0000212 ! choline metabolic pathway
is_a: PW:0000436 ! amine neurotransmitter metabolic pathway

[Term]
id: PW:0000409
name: dopamine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of dopamine that acts as a neurotransmitter and a neurohormone. Dopamine has multiple functions in the brain." [OneLook:www.onelook.com, PMID:19342614]
is_a: PW:0000443 ! catecholamine metabolic pathway

[Term]
id: PW:0000410
name: serotonin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of serotonin - an amine neurotransmitter that is believed to play important roles in a number of conditions such as depression, bipolar disorder, anxiety." [OneLook:www.onelook.com]
is_a: PW:0000444 ! indoleamine and related compounds metabolic pathway

[Term]
id: PW:0000411
name: histamine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of histamine - a biogenic amine that acts as a neurotransmitter and is also involved in the local immune responses." [OneLook:www.onelook.com]
is_a: PW:0000444 ! indoleamine and related compounds metabolic pathway

[Term]
id: PW:0000412
name: gamma-aminobutyric acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of gamma-aminobutyric acid (GABA)." [OneLook:http\://www.onelook.com]
synonym: "GABA metabolism" RELATED []
is_a: PW:0000446 ! inhibitory neurotransmitter metabolic pathway

[Term]
id: PW:0000413
name: heme catabolic pathway
def: "Those metabolic reactions involved in the degradation of heme - an iron-containing compound where the iron is complexed within a porphyrin heterocyclic ring, There are several kinds of hemes depending on the composition of their side chain. Heme serves as a prosthetic group for a number of proteins." [OneLook:www.onelook.com]
is_a: PW:0000221 ! heme metabolic pathway

[Term]
id: PW:0000414
name: protein degradation pathway via the 'core' 20S proteasome pathway
def: "The 'core' 20S proteasome degrades oxidized and/or unfolded proteins in an ATP and ubiquitin independent manner. The association with the 19S regulatory cap yields the 26S proteasome which has substrate selectivity and ATP and ubiquitin-dependent activity." [PMID:9212076;]
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000415
name: proteasome degradation pathway involving cullin-dependent ubiquitin ligases
def: "A proteasome degradation pathway mediated by cullins. Cullins are components of E3 ligase complexes and substrates for Nedd8 - a ubiquitin-like molecule. Neddylation is thought to modulate the activity of cullins." [PMID:10806345, PMID:15021886]
is_a: PW:0000144 ! ubiquitin/proteasome degradation pathway

[Term]
id: PW:0000416
name: sentrinization pathway
def: "A pathway of protein modification via conjugation with sentrin - a family of ubiquitin-like protein. Sentrinization does not target proteins to the proteasome, rather it targets proteins to particular cellular compartments." [PMID:10806345, PMID:15808504]
synonym: "SUMO modification pathway" RELATED []
synonym: "sumoylation pathway" RELATED []
is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules

[Term]
id: PW:0000417
name: ubiquitin, ubiquitin-like/proteasome degradation pathway
def: "The pathway for the ATP-dependent non-lysosomal proteolysis catalyzed by the 26S proteasome and for which ubiquitination, the post-translational covalent conjugation of ubiquitin, or ubiquitin-like, to target proteins is a key signal." [PMID:10993052]
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000418
name: altered ubiquitin, ubiquitin-like degradation pathway
is_a: PW:0000326 ! altered protein degradation pathway
is_a: PW:0000417 ! ubiquitin, ubiquitin-like/proteasome degradation pathway

[Term]
id: PW:0000419
name: water transport pathway
def: "The pathways by which water flows into and out of the cell and into and out of sub-cellular compartments for multi-cellular organisms and mediated by members of the aquaporin family of water channels (WCP). The 13 members identified in mammals are grouped into three subfamilies: aquaporins, selective for water; aquaglyceroporins,  permeable to both water and small molecules; superaquaporins, the sub-cellular aquaporins. WCPs belong to the superfamily of major intrinsic proteins (MIPs)." [GO:0006833, PMID:19165894]
is_a: PW:0000103 ! transport pathway

[Term]
id: PW:0000420
name: altered c-Jun N-terminal kinase MAPK signaling pathway
synonym: "altered JNK signaling pathway" RELATED []
is_a: PW:0000313 ! c-Jun N-terminal kinases MAPK signaling pathway
is_a: PW:0000422 ! altered stress-regulated MAPK signaling pathway

[Term]
id: PW:0000421
name: altered mitogen activated protein kinase pathway
def: "A mitogen activated protein kinase pathway that deviates from what its normal course should be. Altered MAPK pathways have been linked to a spectrum of conditions." [PW InHouse dictionary:InHouse]
synonym: "altered MAPK signaling pathway" RELATED []
is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0001199 ! altered serine/threonine-specific kinase mediated signaling pathway

[Term]
id: PW:0000422
name: altered stress-regulated MAPK signaling pathway
synonym: "altered SAPK pathways" RELATED []
is_a: PW:0000312 ! stress-regulated MAPK signaling pathway
is_a: PW:0000421 ! altered mitogen activated protein kinase pathway

[Term]
id: PW:0000423
name: surfactant homeostasis pathway
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000424
name: altered surfactant homeostasis pathway
def: "A surfactant homeostatic pathway that deviates from what its normal course should be. Mutations in surfactant proteins and in ABCA3 - a member of the ABC transporters have been implicated in the altered pathway and associated with conditions such as Respiratory Distress Syndrome (RDS) in newborns and lung diseases in infants." [PMID:15985750]
is_a: PW:0000358 ! altered homeostasis pathway
is_a: PW:0000423 ! surfactant homeostasis pathway

[Term]
id: PW:0000425
name: diabetic retinopathy pathway
def: "High glucose-mediated oxidative stress effects on the expression of vascular endothelial growth factor are thought to play a role in diabetic retinopathy" [PMID:16026270]
is_a: PW:0000176 ! diabetes pathway

[Term]
id: PW:0000426
name: protein sorting pathway
def: "In the secretory pathway, protein sorting, mainly in trans-Golgi Network (TGN), but also in other compartments, underlies cargo recognition by various carriers to assure the specificity of final localization." [PMID:17686625, PMID:18216874, PMID:18354421]
is_a: PW:0000181 ! pathway pertinent to protein folding, sorting, modification, translocation and degradation
relationship: part_of PW:0000280 ! secretory pathway

[Term]
id: PW:0000427
name: molybdenum cofactor biosynthetic pathway
def: "Molybdenum cofactor is a complex between molybdopterin and an oxide of molybdenum and is required for the activity of several enzymes." [OneLook:http\://www.onelook.com]
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000428
name: altered molybdenum cofactor biosynthetic pathway
is_a: PW:0000427 ! molybdenum cofactor biosynthetic pathway
is_a: PW:0000429 ! altered metabolic pathway of cofactors, vitamins, nutrients

[Term]
id: PW:0000429
name: altered metabolic pathway of cofactors, vitamins, nutrients
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000430
name: killed term
is_obsolete: true

[Term]
id: PW:0000431
name: another killed term
is_obsolete: true

[Term]
id: PW:0000432
name: protein modification pathway
def: "Protein modification pathway exerts a central role in the regulation of protein function and the pathways these function impinge upon. It is also used to target protein for degradation. In the more special aspect of protein modification in the secretory pathway, it involves the final modification of glycoproteins and glycosaminoglycans as well as processing of proteins to their mature forms." [InHouse:InHouse PW dictionary]
is_a: PW:0000181 ! pathway pertinent to protein folding, sorting, modification, translocation and degradation

[Term]
id: PW:0000433
name: protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules
def: "Conjugation of proteins with ubiquitin and ubiquitin-like molecules proceeds via a similar cascade-like, enzyme-driven mechanism but of diverse functionality." [PMID:10806345]
is_a: PW:0000432 ! protein modification pathway

[Term]
id: PW:0000434
name: ubiquitination pathway
def: "A pathway of protein modification via conjugation with ubiquitin. Ubiquitination is primarily involved in targeting protein to the proteasome for degradation. It is also involved in membrane protein trafficking." [PMID:10806345]
is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules

[Term]
id: PW:0000435
name: neddylation pathway
def: "A pathway of protein modification via conjugation with Nedd8  - a ubiquitin-like protein. All Nedd8 targets appear to be members of the cullin family. Cullins participate in the assembly of various E3 ligase complexes. Neddylation pathway is important for embryogenesis and cell cycle control in metazoa, embryonic development in animals." [PMID:10806345, PMID:15021886]
is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules

[Term]
id: PW:0000436
name: amine neurotransmitter metabolic pathway
def: "The prominent examples of biogenic amines are histamine, serotonin, the catecholamine and the choline derived acetylcholine, all acting as neurotransmitters involved in a wide range of processes." [Wikipedia:http\://en.wikipedia.org/wiki/Biogenic_amine]
is_a: PW:0000407 ! neurotransmitter metabolic pathway

[Term]
id: PW:0000437
name: amino acid neurotransmitter metabolic pathway
is_a: PW:0000407 ! neurotransmitter metabolic pathway

[Term]
id: PW:0000438
name: alanine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of alanine. Alanine is a non-essential amino acid with roles in glucose and protein metabolism." [OneLook:www.onelook.com]
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway

[Term]
id: PW:0000439
name: aspartic acid/aspartate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of aspartic acid/aspartate. Aspartic acid is a non-essential amino acid with roles in glucose, protein and nucleotide metabolism. In the brain, it can act as a neurotransmitter." [OneLook:www.onelook.com]
is_a: PW:0000445 ! excitatory neurotransmitter metabolic pathway
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway

[Term]
id: PW:0000440
name: glycine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycine, a non-essential amino acid. Glycine has the simplest structure with a hydrogen atom as its side chain. The amino acid is the major inhibitory neurotransmitter." [OneLook:http\://www.onelook.com]
is_a: PW:0000446 ! inhibitory neurotransmitter metabolic pathway
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway

[Term]
id: PW:0000441
name: epinephrine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of epinephrine - a catecholamine derived from the amino acids phenylalanine and tyrosine. It acts as a hormone and a neurotransmitter." [OneLook:www.onelook.com, PMID:19342614]
synonym: "adrenaline metabolism" RELATED []
is_a: PW:0000443 ! catecholamine metabolic pathway

[Term]
id: PW:0000442
name: norepinephrine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of norepinephrine - a catecholamine derived from the amino acid tyrosine. It acts as a hormone and a neurotransmitter." [OneLook:www.onelook.com, PMID:19342614]
synonym: "noradrenaline metabolism" RELATED []
is_a: PW:0000443 ! catecholamine metabolic pathway

[Term]
id: PW:0000443
name: catecholamine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of catecholamines - chemical compounds derived from tyrosine. Epinephrine, norepinephrine and dopamine are among the most abundant and are produced primarily from the adrenal medulla and the postganglionic fibers of the sympathetic nervous system." [OneLook:www\,onelook.com, PMID:19342614]
is_a: PW:0000211 ! biogenic amines and polyamines metabolic pathway
is_a: PW:0000436 ! amine neurotransmitter metabolic pathway

[Term]
id: PW:0000444
name: indoleamine and related compounds metabolic pathway
def: "Any of a number of indole derivatives containing an amine group." [OneLook:www.onelook.com]
is_a: PW:0000211 ! biogenic amines and polyamines metabolic pathway
is_a: PW:0000436 ! amine neurotransmitter metabolic pathway

[Term]
id: PW:0000445
name: excitatory neurotransmitter metabolic pathway
is_a: PW:0000437 ! amino acid neurotransmitter metabolic pathway

[Term]
id: PW:0000446
name: inhibitory neurotransmitter metabolic pathway
is_a: PW:0000437 ! amino acid neurotransmitter metabolic pathway

[Term]
id: PW:0000447
name: peptide neurotransmitter metabolic pathway
is_a: PW:0000407 ! neurotransmitter metabolic pathway

[Term]
id: PW:0000448
name: neuropeptide Y metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of neuropeptide Y." [OneLook:www.onelook.com]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000449
name: enkephalin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of enkephalin, a pentapeptide involved in the regulation of nociception." [OneLook:www.onelook.com]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000450
name: neurotensin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of neurotensin." [OneLook:www.onelook.com]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000451
name: beta-endorphin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of beta-endorphine - a peptide neurotransmitter that may play a role in depression." [OneLook:www.onelook.com]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000452
name: substance P metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of substance P - a  short-chain polypeptide that acts as a neurotransmitter and a neuromodulator." [OneLook:www\,onelook.com]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000453
name: isoprenoid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of an isoprenoid. Isoprenoids are precursors of both sterols and non-sterol derivatives." [MCW library:QU4 M235b 2009]
synonym: "steroid alcohol" RELATED []
is_a: PW:0000248 ! isoprenoid metabolic pathway

[Term]
id: PW:0000454
name: cholesterol biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of cholesterol, an essential sterol component of mammalian cell membrane." [GO:0006695, OneLook:www.onelook.com, Reactome:REACT_9405.2]
is_a: PW:0001152 ! steroid biosynthetic pathway
is_a: PW:0001304 ! cholesterol metabolic pathway

[Term]
id: PW:0000455
name: excitatory synaptic transmission pathway
def: "Synaptic transmission, or neurotransmission is the pathway of neuron-to-neuron signaling via the chemical synapse and mediated by neurotransmitters. Their effect can be excitatory or inhibitory and many neurotransmitters can exert either effect. The major excitatory neurotransmitter is the amino acid glutamate." [OneLook:www.onelook.com]
synonym: "excitatory neurotransmission pathway" RELATED []
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse

[Term]
id: PW:0000456
name: Inhibitory synaptic transmission pathway
def: "Synaptic transmission, or neurotransmission is the pathway of neuron-to-neuron signaling via the chemical synapse and mediated by neurotransmitters. Their effect can be excitatory or inhibitory and many neurotransmitters can exert either effect. The major inhibitory neurotransmitter is gamma-aminobutyric acid (GABA)." [OneLook:www.onelook.com]
synonym: "Inhibitory neurotransmission pathway" RELATED []
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse

[Term]
id: PW:0000457
name: angiotensin III signaling pathway
def: "Angiotensin III is derived from angiotensin II through the action of aminopeptidase A and in turn is cleaved by aminopeptidase N to generate angiotensin IV. Angiotensin III appears to function in a manner similar to angiotensin II. It plays a role in vasoconstriction and the control of arterial blood pressure. Angiotensin III may be the effective angiotensin peptide in the central nervous system." [PMID:10961935, PMID:11295571]
is_a: PW:0000245 ! angiotensin signaling pathway

[Term]
id: PW:0000458
name: angiotensin IV signaling pathway
def: "Angiotensin IV is derived from angiotensin III through the action of aminopeptidase N. The receptor for angiotensin IV has been shown to be the insulin-regulated membrane aminopeptidase. Studies suggest that angiotensin IV signaling activates a number of intracellular second messenger systems and plays a role in vascular remodeling and memory." [PMID:12591177, PMID:15549174]
is_a: PW:0000245 ! angiotensin signaling pathway

[Term]
id: PW:0000459
name: apelin signaling pathway
def: "Apelin signaling pathway plays a role in the vascular, cardiac, bone and digestive systems as well as the brain." [GO:0060183, PMID:15601620, PMID:15907343]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000460
name: arachidonic acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or conversion of arachidonic acid - a polyunsaturated, omega-6 fatty acid. It is a precursor in the production of eicosanoids and can also be converted to other metabolites, collectively known as the arachidonic acid cascade." [GO:0019369, KEGG:map00590, OneLook:www.onelook.com, PMID:15896353]
synonym: "arachidonic acid cascade" RELATED []
synonym: "KEGG:00590" RELATED []
is_a: PW:0000058 ! fatty acid metabolic pathway

[Term]
id: PW:0000461
name: cyclooxygenase mediated pathway of arachidonic acid metabolism
def: "The cyclooxygenase pathway is one of the three major routes of arachidonic acid oxygenation." [PMID:15896353]
is_a: PW:0000460 ! arachidonic acid metabolic pathway

[Term]
id: PW:0000462
name: lipoxygenase mediated pathway of arachidonic acid metabolism
def: "Lipoxygenase pathway is one of three major routes of arachidonic acid oxygenation" [PMID:15896353]
is_a: PW:0000460 ! arachidonic acid metabolic pathway

[Term]
id: PW:0000463
name: cytochrome P450 monooxygenase mediated pathway of arachidonic acid metabolism
def: "Cytochrome P450 monooxygenase pathway is one the three major routes of arachidonic acid oxygenation." [PMID:15896353]
is_a: PW:0000460 ! arachidonic acid metabolic pathway

[Term]
id: PW:0000464
name: leukotriene metabolic pathway
def: "Those metabolic reactions involving leukotrienes - a class of eicosanoids whose effects include vasoconstriction and bronchoconstriction." [MCW library:QU4 M235b 2009, PMID:15896353]
is_a: PW:0000462 ! lipoxygenase mediated pathway of arachidonic acid metabolism
is_a: PW:0000485 ! eicosanoid metabolic pathway

[Term]
id: PW:0000465
name: hormone signaling pathway
def: "Hormones are a class of molecules that are used as messengers between cells and serve as signals to the target cell. Vertebrate hormones belong to three classes: amine and amino acid derived, peptide and protein hormones, and lipid and phospholipid derived hormones." [OneLook:www.onelook.com]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000466
name: amine and amino acid-derived hormone signaling pathway
is_a: PW:0000465 ! hormone signaling pathway

[Term]
id: PW:0000467
name: peptide and protein hormone signaling pathway
is_a: PW:0000465 ! hormone signaling pathway

[Term]
id: PW:0000468
name: steroid hormone signaling pathway
def: "steroid hormones - steroids that act as hormones - can be grouped into several categories depending on the receptor to which they bind." [OneLook:www.onelook.com]
is_a: PW:0000469 ! lipid hormone signaling pathway

[Term]
id: PW:0000469
name: lipid hormone signaling pathway
def: "The main categories of lipid hormones are the eicosanoids derived from arachidonic acid metabolism and the cholesterol derived steroid hormones." [OneLook:www.onelook.com]
is_a: PW:0000465 ! hormone signaling pathway

[Term]
id: PW:0000470
name: natriuretic peptide signaling pathway
def: "The natriuretic peptide family consists of three peptide hormones of diverse roles in cardiovascular as well as neuroendocrine and renal functions." [PMID:15246247, PMID:15758553, PMID:15911062]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000471
name: atrial natriuretic peptide signaling pathway
def: "Atrial natriuretic peptide hormone pathway plays important roles in the regulation of body fluid volume and blood pressure. " [PMID:15246247, PMID:15758553, PMID:15911062]
synonym: "ANP signaling pathway" RELATED []
is_a: PW:0000470 ! natriuretic peptide signaling pathway

[Term]
id: PW:0000472
name: brain natriuretic peptide signaling pathway
def: "brain natriuretic peptide signaling pathway appears to elicit cardiovascular, renal and endocrine functions similar to those elicited by the atrial natriuretic peptide." [PMID:1524624, PMID:15758553, PMID:15911062]
synonym: "BNP signaling pathway" RELATED []
is_a: PW:0000470 ! natriuretic peptide signaling pathway

[Term]
id: PW:0000473
name: C-type natriuretic peptide signaling pathway
def: "The role of the C-type signaling pathway is not well established. The receptor for the C-type natriuretic peptide, unlike the receptors for the other two types of peptides, is non-guanylyl cyclase receptor that appears to couple to adenylyl cyclase inhibition/phospholipase C activation via Gi family of G-protein. " [PMID:15246247, PMID:15758553, PMID:15911062, PMID:15911072]
synonym: "C-type brain natriuretic peptide signaling pathway" RELATED []
synonym: "CNP signaling pathway" RELATED []
is_a: PW:0000470 ! natriuretic peptide signaling pathway

[Term]
id: PW:0000474
name: coagulation cascade pathway
def: "The coagulation cascade is the series of events proceeding via either the tissue factor or the contact activation pathway and leading to the formation of fibrin clots. The coagulation cascade and the complement pathway of  immune responses are connected in a cross talk. Impaired anticoagulation pathways affect this balanced dialog and lead to various conditions and infections." [GO:0050817, OneLook:www.onelook.com]
synonym: "KEGG:04610" RELATED []
synonym: "secondary hemostasis" RELATED []
relationship: part_of PW:0000475 ! hemostasis pathway

[Term]
id: PW:0000475
name: hemostasis pathway
def: "Hemostasis is the response to blood vessel injury to prevent blood loss via platelet mediated primary homeostasis and the secondary homeostasis of coagulation. The latter is a complex cascade which is triggered by the innate immune response and inflammation." [GO:0007599, Reactome:REACT_604.2, Various:PubMed\, Wikipedia\, Reactome]
synonym: "haemostasis pathway" RELATED []
is_a: PW:0000476 ! cardiovascular system homeostasis pathway

[Term]
id: PW:0000476
name: cardiovascular system homeostasis pathway
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000477
name: natural anticoagulant pathway
is_a: PW:0000476 ! cardiovascular system homeostasis pathway

[Term]
id: PW:0000478
name: tissue factor pathway inhibitor
synonym: "TFPI" RELATED []
is_a: PW:0000477 ! natural anticoagulant pathway

[Term]
id: PW:0000479
name: heparin-antithrombin pathway
is_a: PW:0000477 ! natural anticoagulant pathway

[Term]
id: PW:0000480
name: protein C anticoagulant pathway
is_a: PW:0000477 ! natural anticoagulant pathway

[Term]
id: PW:0000481
name: fibrinolytic cascade pathway
def: "The steps leading to the activation of plasminogen and the subsequent breaking down of a fibrin clot - the product of coagulation cascade." [GO:0042730, PubMed\, OneLook:www.onelook.com]
is_a: PW:0000476 ! cardiovascular system homeostasis pathway

[Term]
id: PW:0000482
name: lipoprotein metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of lipoproteins - any of the protein-lipid complexes. In the blood lipoproteins carry fats essential for the cell. Genetic variability and environmental (nongenetic) factors contribute to alterations in the homeostasis of lipid metabolic pathways and constitute cardiovascular disease risk." [GO:0042157, PMID:16011471, Reactome:REACT_6823.1]
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000483
name: altered lipid metabolic pathway
def: "Those lipid metabolic pathways that deviate from what their normal course should be. Aberrant lipid metabolic pathways, alone or in combination with other pathways underlie a number of diseases." [InHouse:PW InHouse dictionary]
is_a: PW:0000010 ! lipid metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000484
name: altered lipoprotein metabolic pathway
def: "Those lipoprotein metabolic pathways that deviate from what their normal course should be. Aberrant lipoprotein metabolic pathways, alone or in combination with other pathways underlie several diseases." [In House:PW In House dictionary]
is_a: PW:0000482 ! lipoprotein metabolic pathway
is_a: PW:0000483 ! altered lipid metabolic pathway

[Term]
id: PW:0000485
name: eicosanoid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of eicosanoids. Eicosanoids are derived from omega-6 or omega-3 fatty acids and derivatives. Examples include the leukotriene and the prostanoid classes, the latter represented by several families. Eicosanoids play important roles in the immune and vascular systems." [MCW library:QU4 M235b 2009, OneLook:www.onelook.com, PMID:15896353]
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000486
name: class I major histocompatibility complex pathway
def: "Peptides generated from proteolytic degradation of cytosolic proteins are translocated to the ER where they associate with class I MHC molecules. Peptide-class I MHC complexes move through the Golgi and are transported to the cell surface to be recognized by CD8+ T cells." [MCW:Handbook on cellular nad molecular immunology, PMID:16181325]
synonym: "class I MHC pathway" RELATED []
synonym: "MHC class I antigen presentation pathway" RELATED []
is_a: PW:0000825 ! antigen processing and presentation pathway

[Term]
id: PW:0000487
name: class II major histocompatibility complex pathway
def: "Peptides generated from enzymatic degradation of proteins internalized in late endosomes or lysosomes bind to class II MHC molecules. Peptide-class II MHC complexes are delivered to the cell surface to be recognized by CD4+ T cells." [MCW:Handbook on cellular and molecular immunology, PMID:16181322]
synonym: "class II MHC pathway" RELATED []
is_a: PW:0000825 ! antigen processing and presentation pathway

[Term]
id: PW:0000488
name: antigen processing pathway
def: "Antigen processing pathway engages the proteosomal machinery in the cytosol, ER specific proteases as well as chaperones for loading the HMC class I molecules with the 8-10 amino acid peptides" [PMID:16181325]
is_obsolete: true

[Term]
id: PW:0000489
name: angiopoietin signaling pathway
def: "Angiopoietin signaling pathway is involved in the regulation of angiogenic remodeling. Recent studies suggest that the pathway may also be involved in lymphangiogenesis and possibly in the development of hematopoietic system." [PMID:16225862]
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000490
name: transforming growth factor-beta Smad dependent signaling pathway
def: "Transforming growth factor-beta (TGF-beta) signaling is one of the best characterized module of the Tgf-b superfamily pathways. Binding to the type II receptor leads to activation of the type I receptor and subsequent activation of Smad pathway. Nuclear translocation of Smad(s) and interaction with transcription factors rleads to activation or repression of many genes." [PMID:16678165]
synonym: "PID:200227" RELATED []
synonym: "TGF-beta Smad dependent signaling pathway" EXACT []
is_a: PW:0000206 ! transforming growth factor-beta signaling pathway

[Term]
id: PW:0000491
name: vasopressin signaling pathway
def: "The hormone vasopressin plays central roles in cardiovascular and water homeostasis by signaling via two receptor types, G-protein coupled receptors coupling to particular G alpha subunits of heterotrimeric G proteins." [PMID:14624682, PMID:18431594]
synonym: "arginine-vasopressin signaling pathway" RELATED []
synonym: "Avp signaling pathway" RELATED []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000492
name: renin-angiotensin cascade pathway
def: "The renin-angiotensin cascade (RAS) generates a number of bioactive peptides with diverse physiological and pathophysiological functions. RAS exerts vasoconstriction, vasodilation or vascular remodeling, cell proliferation or anti-proliferation effects, depending on which angiotensin peptide generates the signaling. Some of these features are also shared by the kallikrein-kinin system (KKS); the two systems can interact and cross-talk." [KEGG:ko04614, PMID:12676165, PMID:12793984, PMID:15638741, PMID:15883759, PMID:16816138]
synonym: "KEGG:04614" RELATED []
synonym: "RAS system signaling pathway" RELATED []
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000493
name: corticotropin-releasing hormone signaling pathway
def: "Corticotropin-releasing hormone is secreted by the hypothalamus in response to stress or fear and signaling through its receptors stimulates secretion of corticotropic (adrenocorticotropic, ACTH) hormone by the anterior pituitary. ACTH is one of the cleavage products of pro-opiomelanocortin (POMC)." [PMID:20132811]
synonym: "CRH" RELATED []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000494
name: oxytocin signaling pathway
def: "The peptide hormone oxytocin plays a central role in parturition, lactation and sexual behavior." [PMID:14624682]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000495
name: Gas6 - Axl signaling axis
def: "Gas6, a vitamin K-dependent growth factor signals through the Axl subfamily of tyrosine kinase receptors. The Gas6-Axl axis appears to be involved in growth and survival of various cell types as well as in tissue remodeling and regeneration. Deregulation of the axis is involved in a number of conditions, particularly renal." [PMID:11290560, PMID:16285961, PMID:16362042]
synonym: "Gas6-Axl signaling system" RELATED []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000496
name: exogenous pathway
relationship: part_of PW:0000482 ! lipoprotein metabolic pathway

[Term]
id: PW:0000497
name: endogenous pathway
relationship: part_of PW:0000482 ! lipoprotein metabolic pathway

[Term]
id: PW:0000498
name: reverse cholesterol transport pathway
def: "Reverse cholesterol transport (RCT) is the pathway by which cholesterol from extrahepatic cells/tissue is transported to the liver for excretion. The pathway may prevent the development of atherosclerosis by reducing the accumulation of cholesterol in the wall of arteries." [GO:0043691, PMID:16258026]
synonym: "RCT pathway" RELATED []
synonym: "selective cholesterol uptake pathway" RELATED []
is_a: PW:0001346 ! cholesterol transport pathway
relationship: part_of PW:0000482 ! lipoprotein metabolic pathway

[Term]
id: PW:0000499
name: nuclear factor kappa B signaling pathway
def: "NF-kB signaling plays an essential role in the mammalian immune system. The classical/canonical pathway, downstream but not exclusively of tumor necrosis factor/receptor 1 signaling, is regarded as a paradigm of NF-kB signaling. The classical and the non-classical pathway downstream of a subset of Tnf receptor superfamily, share similar sets of core components, albeit in distinct ways. Collectively they regulate the expression of a vast array of genes." [PMID:15371334, PMID:17072321, PMID:18267068]
synonym: "KEGG:04064" RELATED []
synonym: "NF-kappaB signaling pathway" EXACT []
synonym: "NF-kB signaling pathway" RELATED []
synonym: "PID:200021" RELATED []
synonym: "PID:200031" RELATED []
synonym: "PID:200048" RELATED []
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0000818 ! signaling pathway pertinent to immunity
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000500
name: tyrosine-based hormone signaling pathway
is_a: PW:0000466 ! amine and amino acid-derived hormone signaling pathway

[Term]
id: PW:0000501
name: thyroid hormone signaling pathway
def: "Thyroid hormone (TH) signaling pathway plays important roles in glucose and lipid metabolism. The TH receptors are nuclear receptors that once activated act as transcription factors. Low levels of TH stimulate the release of thyrotropin-releasing hormone (TRH) from the hypothalamus, in turn stimulating the secretion of thyroid-stimulating hormone (TSH) from the pituitary whose signaling then triggers TH production. TRH, TSH and TH signaling pathways are part of the hypothalamic-pituitary-thyroid (HPT) axis for which TH itself provides a negative regulatory loop." [PMID:20015660, PMID:20872316, PMID:22759379]
synonym: "TH signaling pathway" EXACT []
is_a: PW:0000500 ! tyrosine-based hormone signaling pathway

[Term]
id: PW:0000502
name: complement system pathway
def: "The complement system is an important effector of innate and also of humoral adaptive immunity. It consists of three biochemical cascades that are differently initiated but share similar late steps and effector functions. The complement pathway and the coagulation cascade are connected in a cross talk. Impaired anticoagulation pathways affect this balanced dialog and lead to various conditions and infections." [KEGG:map04610, MCW library:Handbook on cellular and molecular immunology, PMID:11287977]
synonym: "KEGG:04610" RELATED []
relationship: part_of PW:0000234 ! innate immune response pathway
relationship: part_of PW:0000823 ! humoral immunity pathway

[Term]
id: PW:0000503
name: classical complement pathway
def: "The classical complement pathway is one of the three biochemical pathways of the complement system. It is activated by antigen-bound antibodies." [KEGG:map04610, PMID:11287977]
synonym: "classical pathway" RELATED []
is_a: PW:0000502 ! complement system pathway

[Term]
id: PW:0000504
name: lectin complement pathway
def: "The lectin pathway is one of the three biochemical pathways of the complement system. It is activated by microbial polysaccharides binding to circulating lectins." [GO:0001867, KEGG:map04610, PMID:11287977]
synonym: "lectin pathway" RELATED []
synonym: "mannose-binding lectin pathway" RELATED []
is_a: PW:0000502 ! complement system pathway

[Term]
id: PW:0000505
name: alternative complement pathway
def: "The alternative pathway is one of the three biochemical pathways of the complement system. Stable activation of the alternative pathway occurs on microbial cell surfaces." [GO:0006957, KEGG:map04610, PMID:11287977]
synonym: "alternative pathway" RELATED []
is_a: PW:0000502 ! complement system pathway

[Term]
id: PW:0000506
name: endothelin signaling pathway
def: "Endothelins represent a family of three vasoconstrictor peptides that play a role in several intracellular signaling pathways and have been associated with hypertension, heart failure and myocardial infarction." [PMID:15124920, PMID:16269952]
synonym: "PID:200005" RELATED []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000507
name: estrogen signaling pathway
def: "Estrogens are C18 steroid hormones that constitutes the females sex hormones. Estrogen signals via the estrogen receptor which ones activated drive the expression of target genes." [OneLook:www.onelook.com, PMID:14993442, PMID:19996532]
is_a: PW:0000567 ! sex steroids signaling pathway
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000508
name: platelet aggregation pathway
def: "The pathway involving the attachment of platelets to one another and leading to the formation of a thrombus. Platelets attachment can be induced by a variety of agents." [GO:0070527, PubMed\, OneLook:www.onelook.com]
synonym: "primary hemostasis" RELATED []
relationship: part_of PW:0000475 ! hemostasis pathway

[Term]
id: PW:0000509
name: altered hormone signaling pathway
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000465 ! hormone signaling pathway

[Term]
id: PW:0000510
name: altered insulin-like growth factor signaling pathway
is_a: PW:0000238 ! insulin-like growth factor signaling pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway

[Term]
id: PW:0000511
name: altered peptide and protein hormone signaling pathway
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
is_a: PW:0000509 ! altered hormone signaling pathway

[Term]
id: PW:0000512
name: Interleukin mediated signaling pathway
is_a: PW:0000828 ! cytokine mediated signaling pathway

[Term]
id: PW:0000513
name: interleukin-10 family mediated signaling pathway
def: "The interleukin-10 family comprises several interleukins, including members of the interferon type III also known as interferon lambda or interferon-like type, that carry out various immunomodulatory functions." [PMID:11929132, PMID:20454917, PMID:21112807]
synonym: "Il-10 family mediated signaling pathway" RELATED []
is_a: PW:0000512 ! Interleukin mediated signaling pathway

[Term]
id: PW:0000514
name: interleukin-6 family mediated signaling pathway
def: "Interleukin-6 family includes several members involved in a wide range of biological processes such as immune regulation, inflammation, hematopoiesis and oncogenesis. All members share a common signal transducer, gp130 which activates Jak-Stat and Raf/Mek/Erk signaling pathways." [PMID:20410258, PMID:21715184]
synonym: "Il-6 family mediated signaling pathway" EXACT []
is_a: PW:0000512 ! Interleukin mediated signaling pathway

[Term]
id: PW:0000515
name: Interleukin-10 signaling pathway
def: "Interleukin-10 signaling is involved in various immunomodulatory functions. It promotes the release of immune mediators and antigen presentation exerting important anti-inflammatory effects that may primarily characterize this family member. Signaling by Il-10 and the other members of the family activate the intracellular Jak-Stat cascade." [PMID:20454917, PMID:21115385]
synonym: "Il-10 signaling pathway" RELATED []
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway

[Term]
id: PW:0000516
name: interleukin-6 signaling pathway
def: "Interleukin-6 signaling is involved in a wide range of biological processes such as immune regulation, inflammation, hematopoiesis and oncogenesis. A signal transducer common to all family members, gp130 activates Jak-Stat and Raf/Mek/Erk signaling pathways." [PMID:20303867, PMID:20410258, PMID:21715184]
synonym: "Il-6 signaling pathway" EXACT []
synonym: "PID:200146" RELATED []
is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway
is_a: PW:0000926 ! pro-inflammatory cytokine mediated pathway

[Term]
id: PW:0000517
name: arterial occlusive disease pathway
def: "A pathway leading to a general or specific artery occlusion." [MeSH:Medical Subject Headings]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000518
name: atherosclerosis pathway
def: "A pathway leading to the thickening of medium and large arteries. While lipoprotein related pathways are of interest, monogenic conditions such as those linked to mutations in the laminin gene may also provide clues regarding atherosclerosis pathways." [PMID:15205220]
is_a: PW:0000517 ! arterial occlusive disease pathway

[Term]
id: PW:0000519
name: 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane degradation pathway
def: "Those enzymatic reactions involved in the degradation of DDT - a chlorinated organic insecticide and environmental pollutant. Although it is banned in the United States, it is still widely used in developing countries." [GO:0046701, KEGG:http\://umbbd.msi.umn.edu/ddt/ddt_map.html, KEGG:map00351]
synonym: "DDT degradation pathway" RELATED []
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000520
name: 2,4-dichlorobenzoate degradation pathway
def: "Those enzymatic reactions involved in the degradation of 2,4-dichlorobenzoate - a key intermediate in the aerobic degradation of over 200 polychlorinated biphenyls." [GO:0046298, KEGG:http\://umbbd.msi.umn.edu/dcb/dcb_map.html, KEGG:map00623]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000521
name: 1,2-dichloroethane degradation pathway
def: "Those enzymatic reactions involved in the degradation of 1,2-dichloroethane - a moderately reactive alkylating compound." [KEGG:http\://umbbd.msi.umn.edu/dce/dce_map.html, KEGG:map00631]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000522
name: flavonoid biosynthetic pathway
def: "Those enzymatic reactions involved in the biosynthesis of flavonoids - a class of plant secondary metabolites generally known for their antioxidant activity." [GO:0009813, KEGG:map00941, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000523
name: linoleic acid metabolic pathway
def: "Those enzymatic reactions involved in the synthesis, utilization or degradation of linoleic acid - an unsaturated omega-6 fatty acid. Linoleic acid is an essential fatty acid that humans and other animals cannot synthesize and must obtain from diet." [GO:0043651, KEGG:map00591, OneLook:http\://www.onelook.com]
synonym: "KEGG:00591" RELATED []
is_a: PW:0000058 ! fatty acid metabolic pathway

[Term]
id: PW:0000524
name: heparan sulfate biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of heparan sulfate. Heparan sulfate is a glycosaminoglycan occurring in the cell membrane of most cells. It consists of repeating disaccharide units in specific linkage, each composed of a glucosamine residue linked to an uronic acid, either glucuronic acid or L-iduronic acid, which may be sulfated." [GO:0030210, KEGG:map00534, OneLook:www.onelook.com]
synonym: "KEGG:00534" RELATED []
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway

[Term]
id: PW:0000525
name: Ras mediated signaling pathway
is_a: PW:0000158 ! Ras family mediated signaling pathway

[Term]
id: PW:0000526
name: kallikrein-kinin system signaling pathway
def: "The kallikrein-kinin system (KKA) generates a number of bioactive peptides with diverse physiological and pathophysiological functions. These features are also shared by the renin-angiotensin system (RAS); the two systems can interact and cross-talk." [GO:0002255, PMID:12558525, PMID:12676165, PMID:12793984, PMID:16177542]
synonym: "KKS system signaling pathway" RELATED []
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000527
name: angiotensin II signaling pathway via AT1 receptor
def: "Angiotensin II signaling through the angiotensin type 1 receptor (AT1) activates downstream signaling pathways and elicits a broad range of physiological responses. It is involved in the regulation of blood pressure and volume, water and electrolyte balance and exerts a potent vasoconstrictive effect." [PMID:10977869, PMID:12676164, PMID:16141358]
is_a: PW:0000244 ! angiotensin II signaling pathway

[Term]
id: PW:0000528
name: angiotensin II signaling pathway via AT2 receptor
def: "Angiotensin II signaling through the angiotensin type 2 receptor (AT2) is less well understood and rather controversial. It appears to counteract AT1 receptor function and promote apoptosis. Alternatively, it may complement the effects of AT1 receptor with deleterious consequences in cardiac pathologies. AT2 receptor appears to function in a G-protein dependent as well as independent manner." [PMID:10977869, PMID:12734384, PMID:15158138, PMID:16286568]
is_a: PW:0000244 ! angiotensin II signaling pathway

[Term]
id: PW:0000529
name: angiotensin (1-7) signaling pathway
def: "Angiotensin (1-7) is derived from angiotensin II through the action of angiotensin converting enzyme 2 (ACE2) or from angiotensin I through the action of neutral endopeptidase (NEP). Angiotensin (1-7) signaling appears to have a vasodilatory effect but the exact action of this peptide in humans remains to be established." [PMID:15687842, PMID:15962175, PMID:16520407]
is_a: PW:0000245 ! angiotensin signaling pathway

[Term]
id: PW:0000530
name: angiotensin III signaling pathway via AT1 receptor
def: "Angiotensin III, like angiotensin II, binds to the type 1 and 2 receptors and triggers downstream signaling pathways. In rats, angiotensin III signaling through the receptor type 1 (AT1) can modulate noradrenergic transmission via phospholipase C activation." [PMID:11100981]
is_a: PW:0000457 ! angiotensin III signaling pathway

[Term]
id: PW:0000531
name: angiotensin III signaling pathway via AT2 receptor
def: "The role of angiotensin type 2 receptor is less well understood. In rats, angiotensin III can mediate natriuresis through the activation of receptor type 2." [PMID:16380540]
is_a: PW:0000457 ! angiotensin III signaling pathway

[Term]
id: PW:0000532
name: glycogen biosynthetic pathway
def: "Those metabolic reactions leading to the biosynthesis of glycogen, a highly branched polysaccharide. Glycogen is the storage form of glucose in the cell; it represents an energy reserve that can be mobilized when and where there is a need for glucose." [GO:00005978, OneLook:www.onelook.com, Reactome:REACT_1736.2]
synonym: "glycogenesis" RELATED []
is_a: PW:0000533 ! glycogen metabolic pathway
is_a: PW:0000557 ! glucose storage pathway

[Term]
id: PW:0000533
name: glycogen metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycogen, a highly branched polysaccharide that constitutes the major form of glucose storage in the cell." [InHouse:www.rgd.mcw]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000534
name: glycogen degradation pathway
def: "Those metabolic reactions involved in the breakdown of glycogen to glucose-6-phosphate. Glucose-6-phosphate can then be dephosphorylated to glucose or it can be utilized via glycolysis for energy production; an alternative pathways of G6P utilization is the oxidative phase of the pentose phosphate shunt. A small percentage of glucose-6-phosphate can be converted to hexosamines." [GO:0005980, OneLook:www.onelook.com, Reactome:REACT_1008.1]
synonym: "glycogenolysis " RELATED []
is_a: PW:0000533 ! glycogen metabolic pathway
is_a: PW:0000685 ! glucose biosynthesis pathway

[Term]
id: PW:0000535
name: protein transport pathway
def: "The pathway that mediates the transport of proteins to their proper destination and the trafficking of proteins between organelles." []
is_a: PW:0000103 ! transport pathway

[Term]
id: PW:0000536
name: constitutive secretory pathway
def: "In the constitutive secretory pathway, secreted proteins are sorted into transport vesicles and targeted to their destination in the absence of a signal. It is common to cells that rapidly release their secreted proteins, thus cells other than endocrine and neuroendocrine ones." [GO:0045054, PMID:23182824]
is_a: PW:0000280 ! secretory pathway

[Term]
id: PW:0000537
name: regulated secretory pathway
def: "In the regulated secretory pathway, secreted proteins are sorted into secretory vesicles which are stored intracellularly and move to the final destination upon receiving a signal. It is a salient feature of endocrine and neuroendocrine cells." [GO:0045055, PMID:21907200]
is_a: PW:0000280 ! secretory pathway

[Term]
id: PW:0000538
name: nuclear protein import pathway
is_a: PW:0000535 ! protein transport pathway

[Term]
id: PW:0000539
name: ghrelin system pathway
def: "Ghrelin is an appetite-stimulating hormone secreted primarily from the stomach in response to fasting that can downregulate energy expenditure and lead to weight increase." [PMID:16550252, PMID:17202582]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
relationship: part_of PW:0000357 ! energy homeostasis pathway

[Term]
id: PW:0000540
name: obesity disease pathway
def: "Obesity, usually defined as 20% or more excess body weight, constitutes a major public health problem and an independent risk factor for a number of conditions such as hypertension and diabetes. Deregulation of energy homeostasis, of various metabolic and signaling pathways, genetic and environmental aspects, all can contribute to the development of an obese state." [OneLook:www.onelook.com]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000541
name: signaling pathway involving second messengers
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000542
name: adenosine monophosphate-activated protein kinase (AMPK) signaling pathway
def: "AMPK senses changes in cellular energy as ATP/AMP ratio. AMP binding allosterically activates AMPK; subsequent phosphorylation events lead to repression of energy consuming pathways. One target of AMPK is mTOR signaling pathway. AMPK activates the inhibitory Tsc2 while inhibiting mTorc1 complex." [PMID:15509864, PMID:16885148]
synonym: "5'AMP-activated protein kinase" RELATED []
synonym: "AMPK signaling pathway" RELATED []
is_a: PW:0000541 ! signaling pathway involving second messengers
relationship: part_of PW:0000357 ! energy homeostasis pathway

[Term]
id: PW:0000543
name: protein kinase A (PKA) signaling pathway
def: "Protein kinase A (PKA) signaling is a widely used intracellular pathway and the major route for channeling the cAMP signal. cAMP is regulated by adenylyl cyclases that produce it and phosphodiesterases that hydrolyze it. Compartmentalization of PKA signaling is mediated by the AKAP family of scaffold proteins that bring together the kinase, cAMP modulators and sometimes the targets." [GO:0010737, PMID:14715913, PMID:16214430, Reactome:REACT_15530.1]
synonym: "cAMP-dependent protein kinase A signaling pathway" RELATED []
synonym: "cAMP/PKA signaling pathway" RELATED []
is_a: PW:0000541 ! signaling pathway involving second messengers
is_a: PW:0001194 ! serine/threonine-specific kinase mediated signaling pathway

[Term]
id: PW:0000544
name: altered reverse cholesterol transport pathway
def: "An impaired pathway of reverse cholesterol transport and efflux can pose a risk for the development of cardiovascular disease. This varies in severity and manifestation depending on which gene in the pathway is affected." [PMID:16258026]
synonym: "altered RCT pathway" RELATED []
is_a: PW:0000484 ! altered lipoprotein metabolic pathway
is_a: PW:0000498 ! reverse cholesterol transport pathway
is_a: PW:0001347 ! altered cholesterol transport pathway

[Term]
id: PW:0000545
name: altered transport pathway
is_a: PW:0000103 ! transport pathway
is_a: PW:0000263 ! altered regulatory pathway

[Term]
id: PW:0000546
name: mRNA decay pathway
def: "The pathways of mRNA quality control thereby erroneous mRNA is degraded in the nucleus or cytoplasm, or normal mRNA accumulated in the nucleus is degraded." [GO:0006402, KEGG:map03018, PMID:15933735]
synonym: "KEGG:03015" RELATED []
synonym: "mRNA quality control pathway" EXACT []
synonym: "mRNA surveillance pathway" EXACT []
is_a: PW:0001161 ! RNA degradation pathway

[Term]
id: PW:0000547
name: exosome mediated mRNA decay pathway
def: "The nuclear exosome pathway degrades erroneous mRNA as well as normal mRNA that has accumulated in the nucleus. The exosome is required for processing of other RNA molecules as well." [PMID:15933735, PMID:18786828]
synonym: "exosome mediated mRNA degradation pathway" EXACT []
is_a: PW:0000546 ! mRNA decay pathway

[Term]
id: PW:0000548
name: nonsense-mediated mRNA decay pathway
def: "The nonsense-mediated decay pathway (NMD) degrades mRNA that contains a premature translation termination codon (PTC) and is one of the best characterized systems in eukaryotes." [GO:0000184, PMID:15933735, PMID:17010613]
synonym: "NMD pathway" EXACT []
is_a: PW:0000546 ! mRNA decay pathway

[Term]
id: PW:0000549
name: nonstop mRNA decay pathway
def: "The nonstop mRNA decay pathway degrades mRNA that lacks a translation termination codon." [GO:0070481, PMID:15933735]
synonym: "NSD pathway" EXACT []
is_a: PW:0000546 ! mRNA decay pathway

[Term]
id: PW:0000550
name: Staufen-mediated mRNA decay pathway
def: "Staufen-mediated mRNA decay pathway (SMD) is a rather novel pathway identified in mammals. Staufen (Stau1) is thought to be involved in mRNA localization and it has recently been shown to be involved in mRNA decay. It shares some of the features of the nonsense-mediated mRNA decay pathway (NMD) but does not require components essential for NMD." [PMID:15680326, PMID:15809649, PMID:15933735]
synonym: "SMD pathway" RELATED []
is_a: PW:0000546 ! mRNA decay pathway

[Term]
id: PW:0000551
name: altered mRNA decay pathway
def: "An mRNA decay pathway that deviates from what its normal course should be. An aberrant mRNA decay pathway would lead to the translation of erroneous mRNA with potentially serious consequences." [InHouse PW:InHouse PW]
is_a: PW:0000290 ! altered pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
is_a: PW:0000546 ! mRNA decay pathway

[Term]
id: PW:0000552
name: brassinosteroid biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of brassinosteroids or brassins, a group of plant hormones released in response to low oxygen and sugar, or to root stresses." [GO:0016132, KEGG:map00905, KEGG\, OneLook:http\://www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000553
name: glucose homeostasis pathway
def: "Those pathways involved in the balanced maintenance of  glucose levels, transport and processing as demanded by the needs of the cells, tissues and organs. Glucose is an important and the most efficient fuel source.  Disruption of glucose homeostasis underlies many complex disorders." [GO:0042593, PMID:15466941]
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000554
name: glucose transport pathway
def: "Glucose diffusion into cells requires specific transporter proteins. Two families of hexose transporters facilitate glucose transport down its concentration gradient." [GO:0015758, PMID:15449578, PMID:15466941, Reactome:REACT_212.3]
is_a: PW:0000575 ! sugar transport pathway
relationship: part_of PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000555
name: glucose utilization pathway
def: "The various pathways thereby glucose is oxidized to produce energy, is converted to other molecules or is stored for further use." [PMID:15466941]
relationship: part_of PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000556
name: glucose oxidation pathway
def: "The various pathways thereby glucose is converted to other compounds to yield primarily ATP. The final oxidation of glucose to carbon dioxide and water produces a net of 38 molecules of ATP per molecule of glucose." [PMID:15466941]
is_a: PW:0000555 ! glucose utilization pathway

[Term]
id: PW:0000557
name: glucose storage pathway
def: "Glycogen is the major form of glucose storage. Excess glucose is converted into glycogen - a highly branched polysaccharide. When glucose is rapidly needed, glycogen can be broken down via glycogenolysis." [PMID:15466941]
is_a: PW:0000555 ! glucose utilization pathway

[Term]
id: PW:0000558
name: glucose conversion pathway
is_a: PW:0000555 ! glucose utilization pathway

[Term]
id: PW:0000559
name: hexosamine biosynthetic pathway
def: "The formation of nucleotide hexosamines, primarily UDP-N-acetylglucosamine, constitutes the final step in the hexosamine biosynthetic pathway which provides substrates for the O-linked glycosylation of proteins. Glycoproteins that are either secreted from the cell or inserted into the plasma membrane undergo N-linked glycosylation. The O-linked glycosylation of nuclear and/or cytosolic proteins confers a signaling dimension to the hexosamine biosynthetic pathway." [PMID:15466941, PMID:16885148]
is_a: PW:0000558 ! glucose conversion pathway
is_a: PW:0000570 ! hexosamine metabolic pathway

[Term]
id: PW:0000560
name: facilitative sugar transporter mediated glucose transport pathway
def: "The GLUT family contains 14 members in mammals which can be grouped into 3 classes based on sequence similarities. The members of group I (best characterized) and of group III transporters facilitate glucose transport." [PMID:15449578, PMID:15466941, PMID:17717074, PMID:18171430, PMID:18570632]
synonym: "GLUT mediated glucose transport pathway" RELATED []
is_a: PW:0000554 ! glucose transport pathway

[Term]
id: PW:0000561
name: sodium-glucose cotransporter mediated glucose transport pathway
def: "The sodium-glucose or the sodium-dependent glucose cotransporters are characterized by the presence of 14 transmembrane alpha-helices. The N- and C-termini are responsible for permeating sodium and sugar, respectively." [PMID:15449578, PMID:15466941]
synonym: "SGLT mediated glucose transport pathway" RELATED []
is_a: PW:0000554 ! glucose transport pathway

[Term]
id: PW:0000562
name: growth hormone signaling pathway
def: "The growth hormone signaling pathway is an important regulator of postnatal development. However, despite many years of research, the molecular mechanism underlying its many actions are incompletely understood. It is believed that its actions involve direct and indirect routes. An example of the latter is the role the pathway plays in stimulating the production of insulin-like growth factor." [GO:0060396, PMID:19407495, PMID:8853443]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000563
name: adiponectin signaling pathway
def: "Adiponectin signaling, a hormone secreted by the adipose tissue, impacts on metabolic pathways such as glucose and lipid metabolism, possibly via activation of AMPK pathway. Its deregulation has been linked to obesity, cardiovascular diseases, diabetes and metabolic syndrome." [GO:0033211, PMID:16634986, PMID:16823476, PMID:17140553]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000564
name: androgen signaling pathway
def: "Androgens are C19 steroids that constitutes the male sex hormones. They are also the precursors of female sex hormones, the estrogens. Testosterone and its more potent metabolite, dihydrotestosterone bind to androgen receptors to then translocate to the nucleus and activate the transcription of target genes. Many regulators, both activators and repressors, have been identified. Upregulation of receptor activity has been implicated in prostate cancer." [PMID:17163421, PMID:18657355]
synonym: "PID:200105" RELATED []
is_a: PW:0000567 ! sex steroids signaling pathway
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000565
name: eicosanoid signaling pathway
def: "Eicosanoids are molecules derived from omega-3 or omega-6 fats that can act as hormones. The receptors are G protein coupled (GPCR0 or the nuclear peroxisome proliferator-activated receptor gamma." [OneLook:www.onelook.com]
synonym: "PID:200082" RELATED []
is_a: PW:0000469 ! lipid hormone signaling pathway

[Term]
id: PW:0000566
name: corticosteroid signaling pathway
def: "Corticosteroids group together glucocorticoids and mineralocorticoids, C21-steroid hormones derived from cholesterol. They control a wide range of physiological and cellular responses. Synthetic drugs mimicking their effects are used in the treatment of many conditions. Side effects, long-term use and/or natural deficiencies have been associated with various disorders." [OneLook:www.onelook.com]
is_a: PW:0000468 ! steroid hormone signaling pathway

[Term]
id: PW:0000567
name: sex steroids signaling pathway
def: "Sex steroid mediated signaling pathways have important roles in the development and/or maintenance of sex-specific characteristics or attributes." [OneLook:www.onelook.com]
is_a: PW:0000468 ! steroid hormone signaling pathway

[Term]
id: PW:0000568
name: aldosterone signaling pathway
def: "Aldosterone signaling through the mineralocorticoid receptor plays an important role in the balance of fluids and electrolytes in the body. Its biosynthesis is primarily regulated by the renin-angiotensin system and potassium ions concentration." [PMID:16002531, PMID:17293689]
synonym: "KEGG:04960" RELATED []
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0000783 ! mineralocorticoid signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000569
name: cortisol signaling pathway
def: "Cortisol, also known as hydrocortison, is the most important glucocorticoid. Cortisol signaling, via binding to the glucocorticoid receptor present in almost every animal cell, is essential for many cellular and physiological functions." [OneLook:www.onelook.com]
synonym: "PID:200030" RELATED []
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0000782 ! glucocorticoid signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000570
name: hexosamine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of hexosamines, amino sugars created by adding an amino group to a hexose. Hexosamines, particularly N-acetylglucosamine, are used to modify proteins." [PubMed\, Onelook:NCBI\, www.onelook.com]
is_a: PW:0000152 ! amino sugar metabolic pathway

[Term]
id: PW:0000571
name: neurotrophic factor signaling pathway
def: "Signaling pathways activated by members of the neurotrophic family of growth factors are involved in differentiation of progenitor cells, survival and differentiation of neural cells." [OneLook:www.onelook.com]
synonym: "KEGG:04722" RELATED []
is_a: PW:0000059 ! signaling pathway pertinent to the brain
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000572
name: brain-derived neurotrophic factor signaling pathway
def: "Brain-derived neurotrophic factor signaling pathway plays important roles in the growth, differentiation and survival of neurons." [GO:0031547, OneLook:www.onelook.com]
synonym: "BDNF signaling pathway" EXACT []
is_a: PW:0000571 ! neurotrophic factor signaling pathway

[Term]
id: PW:0000573
name: pentose phosphate pathway - oxidative phase
def: "The oxidative (linear) phase of the pentose phosphate pathway involves the oxidation and decarboxylation of glucose-6-phosphate to produce the 5 carbon sugar ribulose-5-phosphate and the generation of NADPH." [GO:0009051, OneLook:www.oneloook.com, PubMed:http\://www.ncbi.nlm.nih.gov/sites/entrez]
is_a: PW:0000556 ! glucose oxidation pathway
relationship: part_of PW:0000045 ! pentose phosphate pathway

[Term]
id: PW:0000574
name: pentose phosphate pathway - non-oxidative phase
def: "The non-oxidative (circular) phase of the pentose phosphate pathway involves conversion of  ribulose-5-phosphate to ribose-5-phosphate, important in the synthesis of nucleotides and nucleic acid, or to 3 or 6 carbon sugars." [GO:0009052, OneLook:www.oneloook.com, PubMed:http\://www.ncbi.nlm.nih.gov/sites/entrez]
relationship: part_of PW:0000045 ! pentose phosphate pathway

[Term]
id: PW:0000575
name: sugar transport pathway
def: "Those pathways that mediate the transport of sugars across the cell membrane. Transport of glucose, one of the major energy sources in the cell, is an important aspect of sugar transport pathway." [Online\, Pubmed:http\://www.yahoo.com; http\://www.ncbi.nlm.nih.gov/]
synonym: "carbohydrate transport pathway" RELATED []
is_a: PW:0000103 ! transport pathway

[Term]
id: PW:0000576
name: facilitative sugar transporter mediated sugar transport pathway
def: "The GLUT family contains 14 members in mammals which can be grouped into 3 classes based on sequence similarities. These transporters are characterized by the presence of 12 transmembrane alpha helices. Of the 14 members of the GLUT family, 11 have been shown to be involved in sugar transport pathway." [PMID:15449578, PMID:15466941]
synonym: "GLUT mediated sugar transport pathway" RELATED []
is_a: PW:0000575 ! sugar transport pathway

[Term]
id: PW:0000577
name: cytokine and chemokine mediated signaling pathway
def: "Cytokines are small proteins released by the cell and acting as intercellular mediators. Chemokines are a subset of cytokine that can attract and activate leukocytes. They are characterized by a small size and the presence of four cysteines whose location is important for their structural folding. Cytokines or chemokines binding to cognate receptors triggers numerous downstream signaling cascades." [MCW library:Handbook on molecular and cellular immunology]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000578
name: scatter factor/hepatocyte growth factor signaling pathway
def: "Scatter factor/hepatocyte signaling impacts on various biological processes such as proliferation and survival, morphogenesis and motility. SF/HGF and its receptor c-Met have also been implicated in tumor growth and angiogenesis." [GO:0048012, PMID:16212809, PMID:16778093, PMID:18175071]
synonym: "HGF/SF signaling pathway" RELATED []
synonym: "SF/HGF signaling pathway" RELATED []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000579
name: somatostatin signaling pathway
def: "Somatostatin signaling through its receptors regulates processes such as proliferation, secretion and motility via inhibition of growth hormone and factor. The potential anti-tumor activity of somatostatin has led to the development and clinical use of its analogs." [PMID:15078190, PMID:15153426, PMID:15853632, PMID:16625838]
synonym: "somatotropin release inhibitory factor" RELATED []
synonym: "SRIF" RELATED []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000580
name: translation initiation pathway
def: "Translation initiation is the first of the three stages of translation pathway in eukaryotes." [GO:0006413, PMID:17680008]
relationship: part_of PW:0000101 ! translation pathway

[Term]
id: PW:0000581
name: translation elongation pathway
def: "Translation elongation is the second of the three stages of translation pathway in eukaryotes." [GO:0006414, PMID:17680008]
relationship: part_of PW:0000101 ! translation pathway

[Term]
id: PW:0000582
name: translation termination pathway
def: "Translation termination is the third of the three stages of translation pathway in eukaryotes." [GO:0006415, PMID:17680008]
relationship: part_of PW:0000101 ! translation pathway

[Term]
id: PW:0000583
name: orexin/hypocretin signaling pathway
def: "The orexin/hypocretin signaling appears to play a role in the stimulation of food intake. Alterations of the system are associated with the narcolepsy sleep disorder." [OneLook\, PubMed:www.onelook.com, PMID:17299454]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000584
name: altered orexin/hypocretin signaling pathway
def: "An orexin/hypocretin signaling pathway that deviates from what its normal course should be. Alterations in orexin/hypocretin signaling pathway have been linked to narcolepsy. It may also play a role in obesity." [PMID:17299454]
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway
is_a: PW:0000583 ! orexin/hypocretin signaling pathway

[Term]
id: PW:0000585
name: orexin/hypocretin signaling pathway via orexin/hypocretin receptor 1
def: "Orexin/hypocretin signaling through receptor 1 couples to Galphaq class of G proteins. Orexin/hypocretin receptor 1 primarily binds orexin A. Orexin A and B are derived from prepro-orexin precursor." [PMID:17299454]
is_a: PW:0000583 ! orexin/hypocretin signaling pathway

[Term]
id: PW:0000586
name: orexin/hypocretin signaling pathway via orexin/hypocretin receptor 2
def: "Orexin/hypocretin signaling through receptor 2 couples to Galphaq and the inhibitory Galphai classes of G proteins. Orexin/hypocretin receptor 2 binds both orexin A and B derived from the prepro-orexin precursor." [PMID:17299454]
is_a: PW:0000583 ! orexin/hypocretin signaling pathway

[Term]
id: PW:0000587
name: narcolepsy disease pathway
def: "Narcolepsy is a neurological condition characterized by excessive day sleep, an inability to maintain awake states. Dysfunction of the orexin/hypocretin signaling pathway has been linked to this condition." [PMID:17299454]
is_a: PW:0000178 ! neurological disorder disease pathway

[Term]
id: PW:0000588
name: altered adiponectin signaling pathway
def: "An adiponectin signaling pathway that deviates from what its normal course should be. Deregulation of adiponectin signaling have been linked to obesity, cardiovascular diseases, diabetes and metabolic syndrome." [PMID:16634986, PMID:16823476, PMID:17140553]
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway
is_a: PW:0000563 ! adiponectin signaling pathway

[Term]
id: PW:0000589
name: metal homeostasis pathway
def: "Those pathways involved in the proper balance of metal ion levels, uptake and transport, utilization and storage as demanded by the needs of cells, tissues and organs. Disruption of metal ion homeostasis can have toxic and harmful consequences." [InHouse:PW-InHouse]
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000590
name: iron homeostasis pathway
def: "Those pathways involved in the proper balance of iron levels, uptake and transport, utilization and storage as needed by cells, tissues and organs. Iron is essential for many life processes but its reactivity makes it potentially dangerous." [GO:0055072, PMID:17014365, PMID:17194590, PMID:17367269]
is_a: PW:0000589 ! metal homeostasis pathway

[Term]
id: PW:0000591
name: iron transport pathway
is_a: PW:0000593 ! metal ion transport pathway
relationship: part_of PW:0000590 ! iron homeostasis pathway

[Term]
id: PW:0000592
name: iron storage pathway
relationship: part_of PW:0000590 ! iron homeostasis pathway

[Term]
id: PW:0000593
name: metal ion transport pathway
def: "Those pathways that mediate the uptake and transport of metal ions. Metal ion transport pathways are important aspects of metal ion homeostasis." [InHouse:PW-InHouse]
is_a: PW:0001348 ! ion transport pathway

[Term]
id: PW:0000594
name: altered glucose homeostasis pathway
def: "The pathways involved in the balanced maintenance of glucose levels, transport and processing as demanded by the needs of the cells, tissues and organs assure the maintenance of glucose homeostasis. Disruption in these pathways alter glucose homeostasis and underlie many complex disorders - type 2 diabetes and its associated complications is one example." [PMID:15466941]
is_a: PW:0000358 ! altered homeostasis pathway
is_a: PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000595
name: phosphatidylinositol 3-kinase signaling pathway
def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivided into subclass A and B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PMID:16847462, PMID:17052169, PMID:17641274]
synonym: "KEGG:04070" RELATED []
synonym: "phosphoinositide 3-kinase signaling pathway" RELATED []
synonym: "PI3K signaling pathway" RELATED []
is_a: PW:0000541 ! signaling pathway involving second messengers

[Term]
id: PW:0000596
name: altered insulin signaling pathway
def: "An insulin signaling pathway that deviates from what its normal course should be. Deregulation of insulin signaling can have profound health consequences due to its potential to alter glucose and energy homeostasis." [InHouse:PW dictionary]
is_a: PW:0000143 ! insulin signaling pathway
is_a: PW:0000359 ! altered energy homeostasis pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway
is_a: PW:0000594 ! altered glucose homeostasis pathway

[Term]
id: PW:0000597
name: Wnt signaling, non-canonical pathway
def: "The non-canonical Wnt signaling pathway groups the various Wnt signaling routes that are beta-catenin independent." [PMID:16019432, PMID:18432252]
synonym: "beta-catenin independent Wnt signaling pathway" RELATED []
synonym: "PID:200020" RELATED []
is_a: PW:0000008 ! Wnt signaling pathway

[Term]
id: PW:0000598
name: altered Wnt signaling pathway
def: "A Wnt signaling pathway that deviates from what its normal course should be. Deregulation of Wnt signaling has been implicated in several cancers as well as diseases other than cancer." [PMID:18188179, PMID:18432252]
is_a: PW:0000008 ! Wnt signaling pathway
is_a: PW:0000669 ! altered glycoprotein signaling pathway
is_a: PW:0000673 ! altered signaling pathway pertinent to development

[Term]
id: PW:0000599
name: altered Wnt signaling, canonical pathway
def: "A canonical Wnt signaling pathway that deviates from what its normal course should be. Mutations in core components of the canonical pathway have been implicated in several types of cancer as well as diseases other than cancer." [PMID:18188179, PMID:18432252]
is_a: PW:0000201 ! Wnt signaling, canonical pathway
is_a: PW:0000598 ! altered Wnt signaling pathway

[Term]
id: PW:0000600
name: altered Wnt signaling, non-canonical pathway
def: "A non-canonical Wnt signaling pathway that deviates from what its normal course should be. Deregulation of the beta-catenin independent pathway appears to play a role in the biology of tumors." [PMID:18271916]
is_a: PW:0000597 ! Wnt signaling, non-canonical pathway
is_a: PW:0000598 ! altered Wnt signaling pathway

[Term]
id: PW:0000601
name: altered p38 MAPK signaling pathway
is_a: PW:0000198 ! p38 MAPK signaling pathway
is_a: PW:0000422 ! altered stress-regulated MAPK signaling pathway

[Term]
id: PW:0000602
name: altered extracellular signal-regulated Raf/Mek/Erk signaling pathway
def: "A Raf/Mek/Erk signaling pathway that deviates from what its normal course should be. Aberrant Raf/Mek/Erk signaling has been implicated in many types of cancer." [PMID:17126425, PMID:17229475]
is_a: PW:0000102 ! the extracellular signal-regulated Raf/Mek/Erk signaling pathway
is_a: PW:0000421 ! altered mitogen activated protein kinase pathway

[Term]
id: PW:0000603
name: Erk5 MAPK signaling pathway
def: "Erk5 pathway, also known as the big MAP kinase, is activated by various stresses but not by inflammatory cytokines. In HeLa and PC12 cells, the pathway can be activated by growth factors." [GO:0070375, KEGG:map04010, PMID:17229475, PMID:17306385, Reactome:REACT_12020.1]
synonym: "Bmk1 MAPK signaling pathway" RELATED []
is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway

[Term]
id: PW:0000604
name: altered Erk5 MAPK signaling pathway
is_a: PW:0000421 ! altered mitogen activated protein kinase pathway
is_a: PW:0000603 ! Erk5 MAPK signaling pathway

[Term]
id: PW:0000605
name: cancer pathway
def: "Cancer, or malignant neoplasm, represents a category of diseases characterized by uncontrolled cell growth and avoidance of apoptosis, invasion and metastasis.  Deregulation of many pathways - signaling, regulatory, metabolic and combination of them, have been implicated in susceptibility to or development of these conditions. Generally, cancer is classified according to the tissue or organ affected." [PMID:10647931]
synonym: "neoplasm pathway" RELATED []
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000606
name: urogenital cancer pathway
def: "Urogenital cancer groups those malignancies that affect the urinary system and reproductive organs. Deregulation of several pathways along with genetic damage accumulated over time can lead to the development of these conditions." [InHouse:InHouse PW dictionary]
synonym: "genitourinary cancer pathway" RELATED []
synonym: "urinogenital cancer pathway" RELATED []
is_a: PW:0000605 ! cancer pathway

[Term]
id: PW:0000607
name: ovarian cancer pathway
def: "Ovarian cancer is a leading cause of cancer deaths in women. Several susceptibility genes have been identified and they have a role to play in pathways involved in or regulating proliferation, DNA repair and apoptosis." [PMID:12413930, PMID:12886939, PMID:15111296]
synonym: "ovarian neoplasm pathway" RELATED []
is_a: PW:0000606 ! urogenital cancer pathway

[Term]
id: PW:0000608
name: cervical cancer pathway
def: "Cervical cancer affects the cervical area and human papilloma virus (HPV) infection plays a major role in the pathogenesis of the condition. A number of HPV proteins interact with and affect the function of several host proteins that play a role in apoptoptic pathway and/or those involved in cell proliferation." [PMID:10471054, PMID:11486705]
synonym: "cervical neoplasm pathway" RELATED []
is_a: PW:0000606 ! urogenital cancer pathway

[Term]
id: PW:0000609
name: prostate cancer pathway
def: "Prostate cancer is a frequent form of cancer in men over the age of fifty. It is usually asymptomatic but when in an advanced stage, it may spread to other parts of the body causing symptoms others than those sometimes observed. Several susceptibility as well as defective genes have been identified." [KEGG:map05215, PMID:12878745, PMID:14752525, PMID:15149739]
synonym: "KEGG:05215" RELATED []
synonym: "prostate neoplasm pathway" EXACT []
is_a: PW:0000606 ! urogenital cancer pathway

[Term]
id: PW:0000610
name: bladder cancer pathway
def: "Bladder cancer groups several types of malignant tumors of the urinary bladder. It is more prevalent in men than in women and combines both risk factors such as tobacco and exposure to certain carcinogens and genetic factors. Mutations in genes involved in a number of signaling pathways have been implicated in the development of these conditions." [KEGG:map05219, PMID:16474624, PMID:17158541]
synonym: "bladder neoplasm pathway" EXACT []
synonym: "KEGG:05219" RELATED []
is_a: PW:0000606 ! urogenital cancer pathway

[Term]
id: PW:0000611
name: endometrial cancer pathway
def: "Endometrial cancer affects the lining of the uterus, or endometrium. Hormonal and genetic alterations play a role in the development of this carcinoma type. Mutations in genes acting in several pathways have been associated with the condition and its types." [KEGG:map05213, PMID:12583434, PMID:15947972, PMID:16508724]
synonym: "endometrial neoplasm pathway" EXACT []
synonym: "KEGG:05213" RELATED []
is_a: PW:0000606 ! urogenital cancer pathway

[Term]
id: PW:0000612
name: colorectal cancer pathway
def: "Colorectal cancer are malignant tumors of the colon and rectum. Both risk factors usually relating to life style such as physical exercise or use of tobacco and genetics contribute to the development of the condition. Mutations in the components of canonical Wnt and Smad-dependent TGF-beta signaling and of DNA mismatch repair pathways  have been associated with the pathogenesis of colorectal cancer pathway." [KEGG:map05210, OneLook:www.onelook.com]
synonym: "colorectal neoplasm pathway" EXACT []
synonym: "KEGG:05210" RELATED []
is_a: PW:0000627 ! gastrointestinal cancer pathway

[Term]
id: PW:0000613
name: altered transforming growth factor-beta signaling pathway
def: "A trasforming growth factor-beta (TGF-beta) signaling pathway that deviates from what its normal course should be. Altered Tgf-b signaling, primarily the well characterized SMAD dependent pathway, has been implicated in numerous conditions." [PMID:16678165, PMID:18313409]
synonym: "altered TGF-beta signaling pathway" RELATED []
is_a: PW:0000206 ! transforming growth factor-beta signaling pathway
is_a: PW:0000335 ! altered transforming growth factor-beta superfamily mediated signaling pathway

[Term]
id: PW:0000614
name: altered transforming growth factor-beta Smad dependent signaling pathway
def: "A transfoming growth factor-beta Smad dependent signaling pathway that deviates from what its normal course should be. Altered TGF-beta Smad dependent signaling has been implicated in vascular conditions and tumorigenesis." [PMID:18313409]
synonym: "altered TGF-beta Smad dependent signaling pathway" RELATED []
is_a: PW:0000490 ! transforming growth factor-beta Smad dependent signaling pathway
is_a: PW:0000613 ! altered transforming growth factor-beta signaling pathway

[Term]
id: PW:0000615
name: altered bone morphogenetic protein signaling pathway
def: "A bone morphogenetic protein (BMP) signaling pathway that deviates from what its normal course should be. Altered BMP signaling has been implicated in cardiovascular condition, pulmonary hypertension, the juvenile polyposis syndrome (JPS)." [PMID:18313409]
synonym: "altered BMP signaling pathway" RELATED []
is_a: PW:0000330 ! Bone morphogenetic proteins signaling pathway
is_a: PW:0000335 ! altered transforming growth factor-beta superfamily mediated signaling pathway

[Term]
id: PW:0000616
name: altered tumor necrosis factor superfamily mediated signaling pathway
def: "Those tumor necrosis factor superfamily mediated pathways that deviate from what their normal course should be. Altered tumor necrosis factor superfamily pathways have been implicated in a spectrum of conditions ranging from septic shock and tumorigenesis to diabetes, rheumatoid arthritis and various inflammatory diseases." [PMID:11239407, PMID:11796220, PMID:14555214]
synonym: "altered TNF superfamily signaling pathay" RELATED []
is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway
is_a: PW:0000617 ! altered cytokine mediated signaling pathway

[Term]
id: PW:0000617
name: altered cytokine mediated signaling pathway
def: "A cytokine mediated signaling pathway that deviates from what its normal course should be. Aberrant cytokine signaling pathway, alone or in combination with other pathways underlie various diseases." [InHouse:PW dictionary]
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000828 ! cytokine mediated signaling pathway

[Term]
id: PW:0000618
name: altered tumor necrosis factor mediated signaling pathway
def: "A tumor necrosis factor (Tnf) signaling pathway that deviates from what its normal course should be. Altered Tnf signaling has been implicated in many human diseases - cerebral malaria, cancer, multiple sclerosis - are a few examples." [PMID:12040173, PMID:12655295, PMID:14504472]
synonym: "altered TNF signaling pathway" RELATED []
synonym: "altered TNF-alpha signaling pathway" RELATED []
is_a: PW:0000233 ! tumor necrosis factor mediated signaling pathway
is_a: PW:0000616 ! altered tumor necrosis factor superfamily mediated signaling pathway
is_a: PW:0000680 ! altered extrinsic apoptotic pathway

[Term]
id: PW:0000619
name: altered nuclear factor kappa B signaling pathway
def: "A nuclear factor kappa B (NF-kB) signaling pathway that deviates from what its normal course should be. Altered NF-kB signaling has been implicated in a number of conditions including immunodeficiency, inflammation and several forms of cancer." [PMID:17072330, PMID:17072331]
synonym: "altered NF-kappaB signaling pathway" RELATED []
synonym: "altered NF-kB signaling pathway" RELATED []
is_a: PW:0000499 ! nuclear factor kappa B signaling pathway
is_a: PW:0000719 ! altered transcription factor mediated signaling pathway
is_a: PW:0001314 ! altered transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000620
name: altered signaling pathway involving second messengers
def: "Those signaling pathways involving second messengers that deviate from what their normal course should be. Deregulation of these pathways can have far reaching consequences." [InHouse:PW dictionary]
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000541 ! signaling pathway involving second messengers

[Term]
id: PW:0000621
name: altered phosphatidylinositol 3-kinase signaling pathway
is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway
is_a: PW:0000620 ! altered signaling pathway involving second messengers

[Term]
id: PW:0000622
name: altered phosphatidylinositol 3-kinase-Akt signaling pathway
def: "A phosphatidylinositol 3-kinase-Akt signaling pathway that deviates from what its normal course should be. Altered phosphatidylinositol 3-kinase-Akt signaling pathway has been implicated in several forms of cancer. The components of the pathway are attractive targets for the development of therapeutics." [PMID:17952368, PMID:18288939, PMID:18288941, PMID:18473732]
is_a: PW:0000232 ! phosphatidylinositol 3-kinase-Akt signaling pathway
is_a: PW:0000964 ! altered phosphatidylinositol 3-kinase class I signaling pathway
is_a: PW:0001199 ! altered serine/threonine-specific kinase mediated signaling pathway

[Term]
id: PW:0000623
name: altered scatter factor/hepatocyte growth factor signaling pathway
def: "A scatter factor/hepatocyte growth factor signaling pathway that deviates from what its normal course should be. Aberrant Hgf signaling via Met receptor has been implicated in numerous forms of cancer." [PMID:18175071]
synonym: "altered HGF/SF signaling pathway" RELATED []
synonym: "altered SF/HGF signaling pathway" RELATED []
is_a: PW:0000298 ! altered growth factor signaling pathway
is_a: PW:0000578 ! scatter factor/hepatocyte growth factor signaling pathway

[Term]
id: PW:0000624
name: breast cancer pathway
def: "Breast cancer or neoplasm is the most common cancer among women and the second worldwide after lung cancer. Deregulated pathways such estrogen or PI3K-Akt signaling have been implicated in breast cancer. In many cases, the disease is estrogen-dependent and it is possible that dysregulation of miRNA may correlate with the expression of estrogen receptor. Mutations in a number of other genes such as Brca1, 2 and 3 or p53 have also been associated with breast cancer." [OMIM:114480, PMID:17275086, PMID:20739888]
synonym: "breast neoplasm" RELATED []
is_a: PW:0000605 ! cancer pathway

[Term]
id: PW:0000625
name: digestive system cancer pathway
def: "A general term grouping neoplastic pathways of the biliary tract, liver, pancreas and the gastrointestinal system." [MeSH:MeSH, OMIM:OMIM]
synonym: "digestive system neoplasm pathway" RELATED []
synonym: "gastrointestinal neoplasm pathway" RELATED []
is_a: PW:0000605 ! cancer pathway

[Term]
id: PW:0000626
name: pancreatic cancer pathway
def: "Pancreatic cancer, a malignant tumor of the pancreas, has both genetic and predisposing factors. Deregulated pathways, such as TGF-B, PI3K-Akt or RAF/MEK/ERK, have been implicated in the development of pancreatic cancer." [KEGG:map05212, PMID:17898532, PMID:18662538]
synonym: "KEGG:05212" RELATED []
synonym: "pancreatic neoplasm pathway" EXACT []
is_a: PW:0000625 ! digestive system cancer pathway
is_a: PW:0000700 ! endocrine gland cancer pathway

[Term]
id: PW:0000627
name: gastrointestinal cancer pathway
def: "A general term grouping neoplastic pathways of the esophagus, gastric or stomach and intestinal system." [MeSH:MeSH, OMIM:OMIM]
synonym: "gastrointestinal neoplasm pathway" RELATED []
is_a: PW:0000625 ! digestive system cancer pathway

[Term]
id: PW:0000628
name: intestinal cancer pathway
synonym: "intestinal neoplasm pathway" RELATED []
is_a: PW:0000627 ! gastrointestinal cancer pathway

[Term]
id: PW:0000629
name: gastric cancer pathway
def: "Gastric cancer is the fourth most common form of cancer worldwide and has a high death rate. Deregulated pathways, such as Wnt, PI3K-Akt or RAF/MEK/ERK, have been implicated in the development of gastric cancer." [PMID:17203201]
synonym: "gastric neoplasm pathway" RELATED []
synonym: "stomach cancer pathway" RELATED []
synonym: "stomach neoplasm pathway" RELATED []
is_a: PW:0000627 ! gastrointestinal cancer pathway

[Term]
id: PW:0000630
name: liver cancer pathway
synonym: "hepatic cancer pathway" RELATED []
synonym: "hepatic neoplasm pathway" RELATED []
synonym: "liver neoplasm pathway" RELATED []
is_a: PW:0000625 ! digestive system cancer pathway

[Term]
id: PW:0000631
name: head and neck cancer pathway
def: "A general term grouping neoplastic pathways of the upper aerodigestive system. Deregulated pathways, such as TGF-B, PI3K-Akt or epidermal growth factor (EGF) signaling, have been implicated in the of head and neck cancer." [MeSH:MeSH, OMIM:OMIM, PMID:18662538]
synonym: "head and neck neoplasm pathway" RELATED []
is_a: PW:0000605 ! cancer pathway

[Term]
id: PW:0000632
name: bone cancer pathway
synonym: "bone neoplasm pathway" RELATED []
is_a: PW:0000605 ! cancer pathway

[Term]
id: PW:0000633
name: skin cancer pathway
synonym: "skin neoplasm pathway" RELATED []
is_a: PW:0000605 ! cancer pathway

[Term]
id: PW:0000634
name: altered Wnt signaling, the planar cell polarity pathway
def: "A planar cell polarity Wnt signaling pathway that deviates from what its normal course should be. Altered planar cell polarity Wnt signaling has been implicated in a number of conditions including gastric and pancreatic cancer." [PMID:17203201]
synonym: "altered PCP signaling pathway" RELATED []
is_a: PW:0000200 ! Wnt signaling, the planar cell polarity pathway
is_a: PW:0000600 ! altered Wnt signaling, non-canonical pathway

[Term]
id: PW:0000635
name: altered Wnt/calcium signaling pathway
synonym: "altered Wnt/Ca(II) signaling pathway" RELATED []
is_a: PW:0000199 ! the Wnt/calcium signaling pathway
is_a: PW:0000600 ! altered Wnt signaling, non-canonical pathway

[Term]
id: PW:0000636
name: exocytosis pathway
def: "The exocytosis pathway involves trafficking of protein containing secretory vesicles to their final destination. It consists of several steps: budding, transport mediated by microtubule and actin associated molecular motors, tethering/docking and fusion with target membrane. Members of the Arf and Rab family of Ras superfamily are involved in the control of exit from Golgi and exocytic route, respectively." [PMID:16882731, PMID:18354421, PMID:21585247]
relationship: part_of PW:0000280 ! secretory pathway

[Term]
id: PW:0000637
name: protein modification pathway in the secretory pathway
def: "In the secretory pathway, the protein modification pathway involves the appropriate modification of glycoproteins and proteoglycans. It also provides for processing of the pro-forms of proteins into their mature form." [PMID:18354421]
is_a: PW:0000432 ! protein modification pathway
relationship: part_of PW:0000280 ! secretory pathway

[Term]
id: PW:0000638
name: Endoplasmic Reticulum-associated degradation pathway
def: "In the endoplasmic reticulum correctly folded proteins are targeted for further export whereas misfolded proteins are retained and targeted for degradation." [GO:0030433, PMID:18075753, PMID:18216874, PMID:22535891]
synonym: "ERAD pathway" RELATED []
synonym: "KEGG:04141" RELATED []
is_a: PW:0000325 ! protein degradation pathway
relationship: part_of PW:0000280 ! secretory pathway

[Term]
id: PW:0000639
name: insulin responsive facilitative sugar transporter mediated glucose transport pathway
def: "The GLUT family contains 14 members in mammals which can be grouped into 3 classes based on sequence similarities. The members of group I (best characterized) and of group III transporters facilitate glucose transport. Of the three members of group I, Slc2a4 (Glut4), is involved in insulin-mediated uptake of glucose in the heart, skeletal muscle and adipose tissue. The response - central to glucose homeostasis - brings together several signaling and trafficking events." [PMID:15449578, PMID:15466941, PMID:17717074, PMID:18171430, PMID:18570632]
synonym: "PID:200196" RELATED []
is_a: PW:0000560 ! facilitative sugar transporter mediated glucose transport pathway

[Term]
id: PW:0000640
name: glycolysis pathway
def: "The glycolytic pathway converts the six-carbon glucose to two three-carbon pyruvate molecules. The ten reactions of glycolysis can be subdivided into an energy consuming 'stage I' and an energy generating 'stage II'. The net energy yield is two molecules of ATP. Pyruvate can further be oxidized via the citrate cycle, converted to lactose under anaerobic conditions or back to glucose via gluconeogenesis." [GO:0006096, KEGG:map00010, MCW Libraries:Voet & Voet \"Fundamentals od Biochemistry\" 3rd edition, Reactome :REACT_1383.5]
synonym: "Embden-Meyerhof-Parnas pathway" RELATED []
synonym: "KEGG:00010" RELATED []
is_a: PW:0000025 ! glycolysis/gluconeogenesis pathway
is_a: PW:0000556 ! glucose oxidation pathway

[Term]
id: PW:0000641
name: gluconeogenesis pathway
def: "The gluconeogenic pathway involves the synthesis of glucose from noncarbohydrate precursors. They include the glycolysis products pyruvate and lactate, citric acid cycle intermediates and the carbon skeletons of many amino acids." [GO:0006094, KEGG:map00010, MCW Libraries:Voet & Voet \"Fundamentals of Biochemistry\" 3rd edition, Reactome:REACT_1520.3]
synonym: "KEGG:00010" RELATED []
is_a: PW:0000025 ! glycolysis/gluconeogenesis pathway
is_a: PW:0000685 ! glucose biosynthesis pathway

[Term]
id: PW:0000642
name: fatty acid degradation pathway
def: "Fatty acid degradation occurs primarily via beta oxidation in the mitochondrion. It also occurs via the alpha degradation in peroxisomes and the omega degradation which is an alternative pathway. Other pathways include the degradation of branched-chain, unsaturated and odd-chain fatty acids." [MCW libraries:Biochemistry Handbook, MCW libraries:QU4 M235b 2009, PMID:21156023]
is_a: PW:0000058 ! fatty acid metabolic pathway

[Term]
id: PW:0000643
name: altered glycogen metabolic pathway
def: "A glycogen metabolic pathway that deviates from what its normal course should be. Aberrant glycogen metabolism has been associated with several glycogen storage diseases." [MCW libraries:Biochemistry Handbook]
is_a: PW:0000305 ! altered carbohydrate metabolic pathway
is_a: PW:0000533 ! glycogen metabolic pathway

[Term]
id: PW:0000644
name: altered glycogen biosynthetic pathway
def: "A glycogen biosynthetic pathway that deviates from what its normal course should be. Aberrant glycogen metabolism has been associated with several glycogen storage diseases." [MCW libraries:Biochemistry Handbook]
is_a: PW:0000532 ! glycogen biosynthetic pathway
is_a: PW:0000643 ! altered glycogen metabolic pathway

[Term]
id: PW:0000645
name: altered glycogen degradation pathway
def: "A glycogen degradation pathway that deviates from what its normal course should be. Aberrant glycogen metabolism has been associated with several glycogen storage diseases." [MCW libraries:Biochemistry Handbook]
is_a: PW:0000534 ! glycogen degradation pathway
is_a: PW:0000643 ! altered glycogen metabolic pathway

[Term]
id: PW:0000646
name: cell-extracellular matrix signaling pathway
def: "Cell-extracellular matrix signaling pathway conveys information between cells and components of the extracellular matrix using cell adhesion molecules." [RGD:InHouse dictionary]
synonym: "cell-ECM signaling pathway" EXACT []
synonym: "KEGG:04512" RELATED []
is_a: PW:0000648 ! cell adhesion signaling pathway

[Term]
id: PW:0000647
name: forkhead signaling pathway
def: "Forkhead proteins represent a large family of transcription factors that regulate the expression of genes involved in cell growth, proliferation and survival as well as organ development and speech acquisition." [PMID:10702024, PMID:12801727, PMID:15492844, PMID:15516968, PMID:17275054, PMID:18174472, PMID:19274050]
synonym: "forkead box signaling pathway" RELATED []
synonym: "FOX signaling pathway" RELATED []
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling

[Term]
id: PW:0000648
name: cell adhesion signaling pathway
def: "Cell adhesion signaling pathway conveys information between cells or between cells and the extracellular matrix (ECM) using cell adhesion molecules (CAMs). While many CAMs appear to be specialized for either cell-cell or cell-ECM communication, integrin family of receptors mediates both types of signaling." [OneLook:www.onelook.com]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000649
name: <new term>
is_obsolete: true

[Term]
id: PW:0000650
name: signaling pathway pertinent to development
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000651
name: aging pathway
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000652
name: phosphatase mediated signaling pathway
def: "Phosphatases are essential components of biological pathways. Phosphorylaton by protein kinases and dephosphorylation by protein phosphatases exert major regulatory roles. In addition, they can also initiate signaling cascades." [PMID:16132230, PMID:19099538]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000653
name: serine/threonine-specific phosphatase mediated signaling pathway
def: "Serine/threonine-specific phosphatase mediated signaling presents an interesting case. If the number of tyrosine kinases and of tyrosine phosphatases is similar (~100 in mammals), serine/threonine kinases have diversified to some 400 members in the course of evolution while the serine/threonine phosphatases count to about 25. The functional versatility is conferred through the diversity of regulatory subunits with which they interact. The holoenzyme dictates the role the protein complex plays in signaling pathways." [PMID:15780597, PMID:17079133, PMID:19099538]
is_a: PW:0000652 ! phosphatase mediated signaling pathway

[Term]
id: PW:0000654
name: tyrosine-specific phosphatase mediated signaling pathway
def: "The protein tyrosine phosphatase superfamily exerts essential roles in signaling pathways. The coordinated interplay of tyrosine kinase mediated phosphorylation and tyrosine phosphatase mediated dephosphorylation of substrates shape the functional topology of signaling networks. The PTP superfamily is composed of four families." [PMID:15186772, PMID:15817824, PMID:17057753, PMID:19099538]
is_a: PW:0000652 ! phosphatase mediated signaling pathway

[Term]
id: PW:0000655
name: glycoconjugated protein signaling pathway
def: "Those signaling pathways mediated or initiated by oligosaccharide or polysaccharide linked proteins." [OneLook:www\,onelook.com]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000656
name: glycoprotein signaling pathway
def: "Those pathways initiated or mediated by glycoproteins. Glycoproteins have oligosaccharides attached to their amino acid side chains via N- or O-glycosylation. Glycoproteins represent a large category of proteins encompassing a wide range of functionalities." [OneLook:www.onelook.com]
is_a: PW:0000655 ! glycoconjugated protein signaling pathway

[Term]
id: PW:0000657
name: proteoglycan signaling pathway
def: "Those pathways initiated or mediated by proteoglycans - heavily glycosylated proteins that have glycosaminoglycan (GAG) chain(s) linked to their protein cores. GAGs are long unbranched polysaccharides of repeating disaccharide units. Proteoglycans are categorized by the nature of the GAG chain or by their size." [OneLook:www.onelook.com]
is_a: PW:0000655 ! glycoconjugated protein signaling pathway

[Term]
id: PW:0000658
name: glypican signaling pathway
def: "Glypicans are heparan sulfate proteoglycans represented by six families in mammals. They impact on a number of signaling pathways; the effect on signaling can be either inhibitory or stimulatory, depending on the context. They also appear to integrate directional cues important for neuronal migration, axon guidance and synapse formation." [PMID:16937008, PMID:18505598]
synonym: "PID:200026" RELATED []
synonym: "PID:200126" RELATED []
synonym: "PID:200225" RELATED []
is_a: PW:0000657 ! proteoglycan signaling pathway

[Term]
id: PW:0000659
name: syndecan signaling pathway
def: "Syndecan family of proteoglycans appears to be involved in cell-adhesion, particularly cell-extracellular matrix (ECM) signaling and to integrate with the integrin pathway. They also appear to integrate directional cues important for neuronal migration, axon guidance and synapse formation." [PMID:16937008, PMID:17971838]
synonym: "PID:200134" RELATED []
synonym: "PID:200156" RELATED []
synonym: "PID:200192" RELATED []
synonym: "PID:200198" RELATED []
is_a: PW:0000646 ! cell-extracellular matrix signaling pathway
is_a: PW:0000657 ! proteoglycan signaling pathway

[Term]
id: PW:0000660
name: hematopoiesis pathway
def: "Hematopoiesis refers to the formation of blood cellular components. All components are derived from the hematopoietic stem cells residing in the marrow. A great amount of new blood cells needs to be produced daily to maintain steady state levels of circulation." [OneLook:www.onelook.com]
is_a: PW:0000476 ! cardiovascular system homeostasis pathway

[Term]
id: PW:0000661
name: single-strand DNA repair pathway
def: "A DNA repair pathway responsible for removing one or several damaged nucleotides or of  nucleotide mismatched during DNA replication in one of the DNA strands. Several excision pathways are available for correcting single-strand damage." [OneLook:www.onelook.com, PMID:17129767, PMID:23085398]
is_a: PW:0000099 ! DNA repair pathway

[Term]
id: PW:0000662
name: mismatch repair pathway
def: "Mismatch repair pathway assures the maintenance of normal Watson-Crick base pairing. Bases incorrectly matched during DNA replication are removed and replaced with the correct ones." [GO:0006298, KEGG:map03430, OneLook:www.onelook.com]
synonym: "KEGG:03430" RELATED []
synonym: "MMR pathway" EXACT []
is_a: PW:0000661 ! single-strand DNA repair pathway

[Term]
id: PW:0000663
name: double-strand DNA repair pathway
alt_id: PW:0000131
alt_id: PW:0000291
alt_id: PW:0000664
alt_id: PW:0000665
def: "A pathway dealing with repair of double-strand breaks of the DNA or of strand damage such interstrand cross links." [OneLook:www.onelook.com, PMID:23085398]
is_a: PW:0000099 ! DNA repair pathway

[Term]
id: PW:0000666
name: altered single-strand DNA repair pathway
def: "A single-strand DNA repair pathway that deviates from what its normal course should be. Aberrant single-strand repair pathways have been linked to several diseases." [OneLook:www.onelook.com]
is_a: PW:0000292 ! altered DNA repair pathway
is_a: PW:0000661 ! single-strand DNA repair pathway

[Term]
id: PW:0000667
name: altered double-strand DNA repair pathway
is_a: PW:0000292 ! altered DNA repair pathway
is_a: PW:0000663 ! double-strand DNA repair pathway

[Term]
id: PW:0000668
name: altered mismatch repair pathway
def: "A mismatch repair pathway that deviates from what its normal course should be. Mutations in several genes in the pathway have been implicated in cases of colorectal cancer, primarily the inherited forms. To a lesser extent they are found in other types of cancer, such as for instance type 1 endometrial." [PubMed:Several articles]
synonym: "altered MMR pathway" RELATED []
is_a: PW:0000662 ! mismatch repair pathway
is_a: PW:0000666 ! altered single-strand DNA repair pathway

[Term]
id: PW:0000669
name: altered glycoprotein signaling pathway
def: "A glycoprotein signaling pathway that deviates from what its normal course should be." [OneLook:www.onelook.com]
is_a: PW:0000656 ! glycoprotein signaling pathway
is_a: PW:0000670 ! altered glycoconjugated protein signaling pathway

[Term]
id: PW:0000670
name: altered glycoconjugated protein signaling pathway
def: "A glycoconjugated protein signaling pathway that deviates from what its normal course should be." [OneLook:www.onelook.com]
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000655 ! glycoconjugated protein signaling pathway

[Term]
id: PW:0000671
name: altered cell adhesion signaling pathway
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000648 ! cell adhesion signaling pathway

[Term]
id: PW:0000672
name: altered cell-extracellular matrix signaling pathway
is_a: PW:0000671 ! altered cell adhesion signaling pathway

[Term]
id: PW:0000673
name: altered signaling pathway pertinent to development
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000650 ! signaling pathway pertinent to development

[Term]
id: PW:0000674
name: insulin secretion pathway
def: "Insulin secretion by pancreatic beta-cells is an important aspect of glucose homeostasis. A major component of glucose stimulated insulin secretion is represented by the route dependent on the ATP sensitive potassium channels. However, other contributions are also likely to promote insulin secretion." [GO:0030073, PMID:18728221, PMID:18774732, Reactome:REACT_18325.2]
relationship: part_of PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000675
name: glucagon secretion pathway
def: "Glucagon is secreted by pancreatic alpha cell; the mechanisms of its release in response to low glucose levels are poorly understood." [PMID:18522828, PMID:18600596, PMID:18647881]
relationship: part_of PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000676
name: glucagon signaling pathway
def: "Glucagon signaling responds to low levels of circulating glucose to stimulate its release. The action of glucagon signaling is counter-regulatory to the action of insulin and it plays an essential role in glucose homeostasis." [PMID:12626323]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
relationship: part_of PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000677
name: altered insulin secretion pathway
def: "An insulin secretion pathway that deviates from what its normal course should be. Altered insulin secretion has been associated with type 2 diabetes mellitus. Multiple defects are thought to underle malfunctions of insulin secretion; the exact molecular mechanisms are only partially understood." [PMID:18640585]
is_a: PW:0000594 ! altered glucose homeostasis pathway
is_a: PW:0000674 ! insulin secretion pathway

[Term]
id: PW:0000678
name: altered glucagon secretion pathway
def: "A glucagon secretion pathway that deviates from what its normal course should be. Elevated serum glucagon has been observed in patients with type 2 diabetes. The pathway of glucagon secretion is not well understood and this complicates the understanding of how the pathway may falter." [PMID:17623014]
is_a: PW:0000594 ! altered glucose homeostasis pathway
is_a: PW:0000675 ! glucagon secretion pathway

[Term]
id: PW:0000679
name: altered glucagon signaling pathway
def: "A glucagon signaling pathway that deviates from what its normal course should be. Glucagon signaling counteracts the signaling of insulin and the potential exists that an alteration of glucagon signaling has a role to play in diabetes type 2. Serum glucagon is elevated in patients with the disease; the mechanisms leading to and the consequences of elevated glucagon remain to be established." [PMID:17623014]
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway
is_a: PW:0000594 ! altered glucose homeostasis pathway
is_a: PW:0000676 ! glucagon signaling pathway

[Term]
id: PW:0000680
name: altered extrinsic apoptotic pathway
is_a: PW:0000106 ! extrinsic apoptotic pathway
is_a: PW:0000287 ! altered apoptotic cell death

[Term]
id: PW:0000681
name: FasL mediated signaling pathway
def: "Fas ligand binding to its receptor triggers a conformational change that allows the receptor to assemble a signaling complex known as DISC, followed by recruitment of pro-caspase-8 and activation of caspase-3 and -7. It is believed that Fas mediated signaling to elicit apoptosis follows two routes." [PubMed:14744432, Reactome:REACT_900.1]
synonym: "PID:200080" RELATED []
is_a: PW:0000106 ! extrinsic apoptotic pathway
is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway

[Term]
id: PW:0000682
name: Trail mediated signaling pathway
def: "Trail mediated signaling leads to apoptosis via assembly of the DISC complex (Death-Inducing Signaling Complex) downstream of its receptors." [PMID:14744432, Reactome:REACT_402.1]
synonym: "PID:200068" RELATED []
is_a: PW:0000106 ! extrinsic apoptotic pathway
is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway

[Term]
id: PW:0000683
name: integrin mediated cell-cell signaling pathway
def: "A cell-cell signaling pathway mediated by integrins, a family of receptors that convey both 'outside-in' and 'inside-out' signals." [RGD:InHouse dictionary]
is_a: PW:0000286 ! integrin mediated signaling pathway
is_a: PW:0000332 ! cell-cell signaling pathway
created_by: VPetri
creation_date: 2009-08-03T02:43:27Z

[Term]
id: PW:0000684
name: integrin mediated cell-extracellular matrix signaling pathway
def: "A cell-extracellular matrix signaling pathway mediated by integrins, a family of receptors that convey both 'outside-in' and 'inside-out' signals." [RGD:InHouse]
synonym: "integrin mediated cell-ECM signaling pathway" RELATED []
is_a: PW:0000286 ! integrin mediated signaling pathway
is_a: PW:0000646 ! cell-extracellular matrix signaling pathway
created_by: VPetri
creation_date: 2009-08-03T02:45:17Z

[Term]
id: PW:0000685
name: glucose biosynthesis pathway
def: "The metabolic pathways for generating glucose to meet the body's glucose needs. Gluconeogenesis in the liver and to some extent in kidney is the major pathway of glucose production; glycogenolysis is another route for generating glucose in these tissues." [MCW Libraries:ISBN-13 978-0470-12930-2]
relationship: part_of PW:0000553 ! glucose homeostasis pathway
created_by: VPetri
creation_date: 2009-08-05T08:54:36Z

[Term]
id: PW:0000686
name: altered vasopressin signaling pathway
def: "A vasopressin signaling pathway that deviates from what its normal course should be. Altered vasopressin signaling manifests clinically as problems associated with water and sodium balance." [PMID:17761027, PMID:18431594]
is_a: PW:0000491 ! vasopressin signaling pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2009-08-27T09:07:02Z

[Term]
id: PW:0000687
name: altered sugar transport pathway
def: "A sugar transport pathway that deviates from what its normal course should be. Alterations in sugar transport, particularly glucose, can potentially have very harmful consequences." [InHouse:PW dictionary]
is_a: PW:0000545 ! altered transport pathway
is_a: PW:0000575 ! sugar transport pathway
created_by: VPetri
creation_date: 2009-10-07T11:59:25Z

[Term]
id: PW:0000688
name: altered facilitative sugar transporter mediated sugar transport pathway
def: "A facilitative sugar transporter mediated sugar transport pathway that deviates from what its normal course should be. Alterations in sugar transport, particularly glucose, can potentially have very harmful consequences." [InHouse:PW dictionary]
is_a: PW:0000576 ! facilitative sugar transporter mediated sugar transport pathway
is_a: PW:0000687 ! altered sugar transport pathway
created_by: VPetri
creation_date: 2009-10-07T12:05:27Z

[Term]
id: PW:0000689
name: altered glucose transport pathway
def: "A glucose transport pathway that deviates from what its normal course should be. Alterations in glucose transport can potentially have very harmful consequences." [InHouse:PW dictionary]
is_a: PW:0000554 ! glucose transport pathway
is_a: PW:0000594 ! altered glucose homeostasis pathway
is_a: PW:0000687 ! altered sugar transport pathway
created_by: VPetri
creation_date: 2009-10-07T12:08:39Z

[Term]
id: PW:0000690
name: altered facilitative sugar transporter mediated glucose transport pathway
def: "A facilitative sugar transporter mediated glucose transport pathway that deviates from what its normal course should be. Alterations in glucose transport can potentially have very harmful consequences." [InHouse:PW dictionary]
is_a: PW:0000560 ! facilitative sugar transporter mediated glucose transport pathway
is_a: PW:0000689 ! altered glucose transport pathway
created_by: VPetri
creation_date: 2009-10-07T12:12:44Z

[Term]
id: PW:0000691
name: altered sodium-glucose cotransporter mediated glucose transport pathway
def: "A sodium-glucose cotransporter mediated glucose transport pathway that deviates from what its normal course should be. Alterations in glucose transport can potentially have very harmful consequences." [InHouse:PW]
is_a: PW:0000561 ! sodium-glucose cotransporter mediated glucose transport pathway
is_a: PW:0000689 ! altered glucose transport pathway
created_by: VPetri
creation_date: 2009-10-07T12:21:13Z

[Term]
id: PW:0000692
name: altered insulin responsive facilitative sugar transporter mediated glucose transport pathway
def: "An insulin responsive facilitative sugar transporter mediated glucose transport pathway that deviates from what its normal course should be. Alterations in the pathway can manifest in insulin resistance, a hallmark of type 2 diabetes." [PMID:17629673]
is_a: PW:0000639 ! insulin responsive facilitative sugar transporter mediated glucose transport pathway
is_a: PW:0000690 ! altered facilitative sugar transporter mediated glucose transport pathway
created_by: VPetri
creation_date: 2009-10-07T12:24:18Z

[Term]
id: PW:0000693
name: biphenyl degradation pathway
def: "Those enzymatic reactions involved in the degradation of biphenyl, an aromatic hydrocarbon used as a starting material for the production of polychlorinated biphenyls or as an intermediate for the production of a variety of organic compounds." [KEGG:map00621, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway
created_by: VPetri
creation_date: 2009-10-20T08:59:23Z

[Term]
id: PW:0000694
name: geraniol degradation pathway
def: "Those enzymatic reactions involved in the degradation of geraniol, a monoterpenoid and an alcohol, used in perfumes and in flavors." [KEGG:map00281, OneLook:www.onelook.com]
is_a: PW:0000107 ! xenobiotics biodegradation pathway
created_by: VPetri
creation_date: 2009-10-20T09:30:32Z

[Term]
id: PW:0000695
name: <new term>
is_obsolete: true
created_by: VPetri
creation_date: 2009-10-20T10:20:07Z

[Term]
id: PW:0000696
name: zeatin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of zeatin - a plant hormone derived from adenine. It induces plant growth and has been reported to have anti-aging effects on human skin fibroblasts." [GO:0033398, KEGG:map00908, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites
created_by: VPetri
creation_date: 2009-10-20T10:23:22Z

[Term]
id: PW:0000697
name: carotenoid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of carotenoids, organic pigments found in plants and other photosynthetic organisms. Some can act as antioxidants." [GO:0016120, KEGG:map00906, OneLook:www.onelook.com]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites
created_by: VPetri
creation_date: 2009-10-20T10:29:04Z

[Term]
id: PW:0000698
name: thyroid cancer pathway
def: "Thyroid cancer refers to one of several types of malignant tumors of the thyroid gland of which the papillary thyroid cancer is the most frequent accounting for almost 80% of all cases. The other types include follicular, medullary and anaplastic." [KEGG:map05216, OneLook:www.onelook.com]
synonym: "KEGG:05216" RELATED []
synonym: "thyroid neoplasm pathway" EXACT []
is_a: PW:0000631 ! head and neck cancer pathway
is_a: PW:0000700 ! endocrine gland cancer pathway
created_by: vpetri
creation_date: 2009-10-28T01:33:42Z

[Term]
id: PW:0000699
name: parathyroid cancer pathway
def: "Parathyroid cancer is a rare type of cancer whose causes are unknown. There are four parathyroid glands, each of the two lobes of the thyroid gland houses two." [OneLook:www.onelook.com]
is_a: PW:0000631 ! head and neck cancer pathway
created_by: vpetri
creation_date: 2009-10-28T01:39:16Z

[Term]
id: PW:0000700
name: endocrine gland cancer pathway
synonym: "endocrine gland neoplasm pathway" RELATED []
is_a: PW:0000605 ! cancer pathway
created_by: vpetri
creation_date: 2009-10-28T01:48:29Z

[Term]
id: PW:0000701
name: thoracic cancer pathway
synonym: "thoracic neoplasm pathway" RELATED []
is_a: PW:0000605 ! cancer pathway
created_by: vpetri
creation_date: 2009-10-28T01:55:10Z

[Term]
id: PW:0000702
name: respiratory tract cancer pathway
synonym: "respiratory tract neoplasm pathway" RELATED []
is_a: PW:0000701 ! thoracic cancer pathway
created_by: vpetri
creation_date: 2009-10-28T01:57:08Z

[Term]
id: PW:0000703
name: lung cancer pathway
def: "Lung cancer is one of the most common cause of cancer-related death in men but also very common in women. The main types are represented by small cell and non-small cell lung carcinomas. The former tends to respond better to chemotherapy; the latter is at times treated surgically." [OneLook:www.onelook.com]
synonym: "lung neoplasm pathway" RELATED []
is_a: PW:0000702 ! respiratory tract cancer pathway
created_by: vpetri
creation_date: 2009-10-28T02:00:27Z

[Term]
id: PW:0000704
name: small cell lung cancer pathway
def: "Small cell lung cancer is an aggressive type of lung cancer. Several pathways appear to be deregulated and they include the intrinsic apoptotic pathway, PI3K-Akt signaling and changes in oncogene transcription factors such as Myc and p53." [KEGG:map05222, OneLook:www.onelook.com]
synonym: "KEGG:05222" RELATED []
synonym: "SCLC pathway" EXACT []
synonym: "small cell lung neoplasm pathway" EXACT []
is_a: PW:0000703 ! lung cancer pathway
created_by: vpetri
creation_date: 2009-10-28T02:00:59Z

[Term]
id: PW:0000705
name: non-small cell lung cancer pathway
def: "Non-small cell lung cancer groups together several non-small cell lung carcinomas. The main types are represented by squamous cell, adeno- and large-cell carcinoma. Alterations in Ras and epidermal growth factors signaling, among others, have been implicated in the condition." [KEGG:map05223, OneLook:www.onelook.com]
synonym: "KEGG:05223" RELATED []
synonym: "non-small cell lung neoplasm pathway" EXACT []
synonym: "NSCLC pathway" EXACT []
is_a: PW:0000703 ! lung cancer pathway
created_by: vpetri
creation_date: 2009-10-28T02:45:27Z

[Term]
id: PW:0000706
name: leukemia pathway
def: "Leukemia is a cancer of the blood or bone marrow. The term covers a broad spectrum of conditions subdivided by proliferation type - acute and chronic, and by cell type - myeloid and lymphocytic leukemia." [OneLook:www.onelook..com]
is_a: PW:0000605 ! cancer pathway
created_by: vpetri
creation_date: 2009-10-28T03:34:16Z

[Term]
id: PW:0000707
name: myeloid leukemia pathway
def: "Myeloid leukemia affects cells of the myeloid lineage and their precursors and in turn is subdivided by proliferation type." [OneLook:www.onelook.com]
is_a: PW:0000706 ! leukemia pathway
created_by: vpetri
creation_date: 2009-10-28T03:55:53Z

[Term]
id: PW:0000708
name: lymphoid leukemia pathway
def: "Lymphoid leukemia affects lymphoid tissues and there are increase numbers of circulating lymphoblasts and lymphocytes." [OneLook:www.onelook.com]
synonym: "lymphocytic leukemia pathway" RELATED []
is_a: PW:0000706 ! leukemia pathway
created_by: vpetri
creation_date: 2009-10-28T04:33:38Z

[Term]
id: PW:0000709
name: acute myeloid leukemia pathway
def: "Acute myeloid leukemia is a common type of leukemia among adults. Abnormal cells are present inside the bone marrow that grow very vast and replace healthy blood cells. Several signaling pathways are disrupted and/or constitutively activated." [KEGG:map05221, OneLook :www.onelook.com]
synonym: "KEGG:05221" RELATED []
is_a: PW:0000707 ! myeloid leukemia pathway
created_by: vpetri
creation_date: 2009-10-28T04:39:13Z

[Term]
id: PW:0000710
name: chronic myeloid leukemia pathway
def: "Chronic myeloid leukemia, a slowly progressing condition, is a type of leukemia where too many white blood cells are made in the bone marrow." [KEGG:map05220, OneLook:www.onelook.com]
synonym: "KEGG:05220" RELATED []
is_a: PW:0000707 ! myeloid leukemia pathway
created_by: vpetri
creation_date: 2009-10-28T04:39:38Z

[Term]
id: PW:0000711
name: glioma pathway
def: "Gliomas are tumors of the brain categorized by the type of cell they are associated with, their location and grade. Several pathways appear to be deregulated via amplifications, overexpression, mutations or loss." [OneLook:www.onelook.com]
synonym: "KEGG:05214" RELATED []
is_a: PW:0000605 ! cancer pathway
created_by: vpetri
creation_date: 2009-10-29T04:24:22Z

[Term]
id: PW:0000712
name: vasopressin signaling pathway via receptor type 1
def: "Vasopressin signaling via receptor type 1 couples to Gq alpha subunit leading to stimulation of phospholipase C beta, subsequent generation of second messengers and increase in intracellular calcium resulting in vasoconstriction." [PMID:11091117, PMID:14624682]
is_a: PW:0000491 ! vasopressin signaling pathway
created_by: vpetri
creation_date: 2009-11-03T08:25:33Z

[Term]
id: PW:0000713
name: vasopressin signaling pathway via receptor type 2
def: "Vasopressin signaling via receptor type 2 plays a central role in water homeostasis by regulating the translocation of Aqp2 channel. The receptor couples to Gs alpha subunit leading to activation of adenylyl cyclase, production of cyclic AMP and triggering of protein kinase A (PKA) signaling pathway. PKA regulates both the translocation and the expression of the channel." [PMID:11091117, PMID:14624682, PMID:17761027, PMID:18431594]
synonym: "KEGG:04962" RELATED []
is_a: PW:0000491 ! vasopressin signaling pathway
created_by: vpetri
creation_date: 2009-11-03T08:39:15Z

[Term]
id: PW:0000714
name: altered vasopressin signaling pathway via receptor type 1
def: "A vasopressin, receptor type 1 mediated signaling pathway, that deviates from what its normal course should be. Alterations in this pathway might relate to septic shock." [PMID:17133186]
is_a: PW:0000686 ! altered vasopressin signaling pathway
is_a: PW:0000712 ! vasopressin signaling pathway via receptor type 1
created_by: vpetri
creation_date: 2009-11-03T08:51:23Z

[Term]
id: PW:0000715
name: altered vasopressin signaling pathway via receptor type 2
def: "A vasopressin, receptor type 2 mediated signaling pathway, that deviates from what its normal course should be. Alterations in the pathway have been associated with Nephrogenic Diabetes Insipidus (NDI) caused by mutations in the receptor or, more rarely, in aquaporin channel 2." [PMID:17761027]
is_a: PW:0000686 ! altered vasopressin signaling pathway
is_a: PW:0000713 ! vasopressin signaling pathway via receptor type 2
created_by: vpetri
creation_date: 2009-11-03T09:09:09Z

[Term]
id: PW:0000716
name: transcription factor mediated signaling pathway
def: "Transcription factors mediated signaling are components of transcription that, by controlling the expression of target genes, impact upon a wide range of processes." [InHouse:PW dictionary]
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2009-11-30T01:34:55Z

[Term]
id: PW:0000717
name: forkhead class O signaling pathway
def: "The signaling pathway mediated by the FoxO subgroup of forkhead family of transcription factors regulates cell cycle and survival via the expression of its target genes. FoxO pathway is negatively regulated by PI3K-Akt pathway downstream of insulin signaling. It is positively regulated by the Jnk pathway of stress activated MAPK cascade." [PMID:10702024, PMID:17275054, PMID:19274050, PMID:23325358]
synonym: "FoxO signaling pathway" EXACT []
is_a: PW:0000647 ! forkhead signaling pathway
created_by: VPetri
creation_date: 2009-11-30T01:42:57Z

[Term]
id: PW:0000718
name: p53 signaling pathway
def: "p53 transcription factor is a tumor suppressor frequently mutated in cancer. p53 is at the hub of many signaling and regulatory pathways. In response to various stresses, it promotes apoptosis, cell cycle arrest and other defense pathways via transcription dependent as well as independent routes. A key regulator of p53 is Mdm2. Mdm2 is a transcriptional target of p53 thus providing a negative feedback loop." [PMID:18783169, PMID:18927276, PMID:19007744, PMID:19407794, PMID:19776744]
synonym: "KEGG:04115" RELATED []
synonym: "PID:200206" RELATED []
is_a: PW:0000237 ! stress response pathway
is_a: PW:0000303 ! p53-dependent G1/S DNA damage checkpoint pathway
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2009-11-30T03:01:53Z

[Term]
id: PW:0000719
name: altered transcription factor mediated signaling pathway
def: "A transcription factor mediated signaling pathway that deviates from what its normal course should be. Deregulation of such pathways has been linked to cancer and various other diseases." [InHouse:PW dictionary]
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000716 ! transcription factor mediated signaling pathway
created_by: VPetri
creation_date: 2009-11-30T03:40:53Z

[Term]
id: PW:0000720
name: altered p53 signaling pathway
def: "A p53 signaling pathway that deviates from what its normal course should be. Due to its central role at the intersection of many cellular pathways, disturbance of p53 network can have far-reaching negative consequences. The tumor suppressor Tp53 gene is frequently mutated in cancer." [PMID:19776744]
is_a: PW:0000718 ! p53 signaling pathway
is_a: PW:0000719 ! altered transcription factor mediated signaling pathway
is_a: PW:0001314 ! altered transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2009-11-30T03:43:14Z

[Term]
id: PW:0000721
name: nicotine pathway
def: "The pharmacokinetics and pharmacodynamics pathway of nicotine, an alkaloid found in tobacco plants, acting as a stimulant drug in humans and one of the main factors responsible for tobacco dependence." [PharmGKB:http\://www.pharmgkb.org/pathway/PA162355621]
is_a: PW:0000923 ! nervous system drug pathway
created_by: VPetri
creation_date: 2010-01-18T03:34:19Z

[Term]
id: PW:0000722
name: warfarin drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of warfarin. Warfarin is used as anticoagulant that antagonizes the vitamin K dependent clotting pathway. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000922 ! blood and blood forming organs drug pathway
created_by: VPetri
creation_date: 2010-01-18T03:34:31Z

[Term]
id: PW:0000723
name: anti-diabetic drug pathway
def: "The pharmacokinetics and pharmacodynamics of anti-diabetic drugs such as repaglinide, nateglinide and sulfonylurea - inhibitors of ATP-dependent potassium channel. By blocking the channel they stimulate insulin secretion to lower blood glucose level. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/, PMID:11259325, PMID:12919179]
is_a: PW:0000921 ! alimentary tract and metabolism drug pathway
created_by: VPetri
creation_date: 2010-01-18T03:43:49Z

[Term]
id: PW:0000724
name: statin drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of statin. Statins are a class of drugs used to lower cholesterol. They act as inhibitors of HMG-CoA reductase, the enzyme that catalyzes an early rate-limiting step in cholesterol biosynthesis. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000920 ! cardiovascular system drug pathway
created_by: VPetri
creation_date: 2010-01-19T10:48:44Z

[Term]
id: PW:0000725
name: potassium channel inhibitors pharmacodynamics pathway
def: "The pathway of anti-diabetic drugs-target interaction and of the biochemical or physiological responses to them. Repaglinide, nateglinide and sulfonylurea are used as inhibitors of ATP-dependent potassium channel. By blocking the channel they stimulate insulin secretion to lower blood glucose level. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000723 ! anti-diabetic drug pathway
created_by: VPetri
creation_date: 2010-01-20T12:12:30Z

[Term]
id: PW:0000726
name: repaglinide pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of repaglinide. The drug is used as an inhibitor of ATP-dependent potassium channel. By blocking the channel it stimulates insulin secretion to lower blood glucose level. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/, PMID:12919179]
is_a: PW:0000723 ! anti-diabetic drug pathway
created_by: VPetri
creation_date: 2010-01-20T12:14:07Z

[Term]
id: PW:0000727
name: nateglinide pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of nateglinide. The drug is used as an inhibitor of ATP-dependent potassium channel. By blocking the channel it stimulates insulin secretion to lower blood glucose level. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/, PMID:11259325]
is_a: PW:0000723 ! anti-diabetic drug pathway
created_by: VPetri
creation_date: 2010-01-20T12:15:46Z

[Term]
id: PW:0000728
name: statin pharmacodynamics pathway
def: "The pathway of statins-target interaction and of the biochemical or physiological responses to them. Statins are a class of drugs used to lower cholesterol. They act as inhibitors of HMG-CoA reductase, the enzyme that catalyzes an early rate-limiting step in cholesterol biosynthesis. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000724 ! statin drug pathway
created_by: VPetri
creation_date: 2010-01-20T12:21:51Z

[Term]
id: PW:0000729
name: statin pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of statin. Statins are a class of drugs used to lower cholesterol. They act as inhibitors of HMG-CoA reductase, the enzyme that catalyzes an early rate-limiting step in cholesterol biosynthesis. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000724 ! statin drug pathway
created_by: VPetri
creation_date: 2010-01-20T12:22:12Z

[Term]
id: PW:0000730
name: warfarin pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of warfarin. Warfarin is used as anticoagulant that antagonizes the vitamin K dependent clotting pathway. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000722 ! warfarin drug pathway
created_by: VPetri
creation_date: 2010-01-20T12:42:35Z

[Term]
id: PW:0000731
name: warfarin pharmacodynamics pathway
def: "The pathway of warfarin-target interaction and of the biochemical or physiological responses to drug. Warfarin is used as anticoagulant that antagonizes the vitamin K dependent clotting pathway. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000722 ! warfarin drug pathway
created_by: VPetri
creation_date: 2010-01-20T12:42:55Z

[Term]
id: PW:0000732
name: thromboxane metabolic pathway
def: "Those metabolic reactions involving thromboxanes - a family of prostanoid eicosanoids whose effects include vasoconstriction and platelet aggregation." [MCW library:QU4 M235b 2009]
is_a: PW:0001240 ! prostanoid metabolic pathway
created_by: VPetri
creation_date: 2010-02-17T11:26:21Z

[Term]
id: PW:0000733
name: glycosphingolipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycosphingolipids - glycolipids with sugar(s) attached to the ceramide core. Based on the sequences of the core carbohydrate residues, they are classified into a number of series such as lacto- and neolacto-, globo-, ganglio- or muco-series." [GO:0006687, MCW library:QU4 M235b 2009, PMID:15207828, PMID:17976918, PMID:18845618]
synonym: "glycolipid metabolic pathway" RELATED []
synonym: "GSL metabolic pathway" RELATED []
is_a: PW:0000197 ! sphingolipid metabolic pathway
created_by: VPetri
creation_date: 2010-02-17T02:03:36Z

[Term]
id: PW:0000734
name: cerebroside metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of cerebroside, sphingolipids in which the sugar is a monosaccharide." [MCW library:QU4 M235b 2009]
is_a: PW:0000733 ! glycosphingolipid metabolic pathway
created_by: VPetri
creation_date: 2010-02-17T02:05:26Z

[Term]
id: PW:0000735
name: altered sphingolipid metabolic pathway
def: "A sphingolipid metabolic pathway that deviates from what its normal course should be. Altered sphingolipid metabolism has been associated with several lysosomal storage diseases and most appear to be fatal." [MCW library:QU4 M235b 2009, PW dictionary:InHouse dictionary]
is_a: PW:0000197 ! sphingolipid metabolic pathway
is_a: PW:0000483 ! altered lipid metabolic pathway
created_by: VPetri
creation_date: 2010-02-17T02:08:31Z

[Term]
id: PW:0000736
name: triacylglycerol biosynthetic pathway
def: "The de novo synthesis of triacylglycerol, the common form of fatty acid transport and storage. Most triacylglycerols are synthesized in the liver and stored in the adipose tissue." [GO:0019432, MCW library:QU4 M235b 2009]
synonym: "lipogenesis pathway" RELATED []
is_a: PW:0000153 ! triacylglycerol metabolic pathway
created_by: VPetri
creation_date: 2010-02-17T02:15:19Z

[Term]
id: PW:0000737
name: triacylglycerol degradation pathway
def: "The degradation pathway of triacylglycerols when the energy reserves are low such as in the fasting state, during exercise or in response to stress. Triacylglycerols are the common form of fatty acid transport and storage." [GO:0019433, MCW library:QU4 M235b 2009]
synonym: "lipolysis pathway" RELATED []
is_a: PW:0000153 ! triacylglycerol metabolic pathway
created_by: VPetri
creation_date: 2010-02-17T02:19:06Z

[Term]
id: PW:0000738
name: fatty acid beta degradation pathway
def: "Fatty acid degradation via beta oxidation, the most common fatty acid degradation pathway, occurs in four reactions resulting in the formation of acetyl-CoA and a fatty acyl-CoA two carbon shorter than the one that began the cycle. Acetyl-CoA can undergo further oxidation via the Krebs cycle or can be converted to ketone bodies." [MCW library:QU4 M235b 2009]
synonym: "fatty acid beta oxidation pathway" RELATED []
is_a: PW:0000642 ! fatty acid degradation pathway
created_by: VPetri
creation_date: 2010-02-17T02:50:24Z

[Term]
id: PW:0000739
name: fatty acid alpha degradation pathway
def: "The degradation of branched-chain fatty acids is carried out by the alpha oxidation pathway. In humans, this pathway occurs in peroxisomes." [MCW library:QU4 M235b 2009]
synonym: "fatty acid alpha oxidation pathway" RELATED []
is_a: PW:0000642 ! fatty acid degradation pathway
created_by: VPetri
creation_date: 2010-02-17T03:02:55Z

[Term]
id: PW:0000740
name: unsaturated fatty acid degradation pathway
def: "The pathway of unsaturated fatty acids requires additional enzymes." [MCW library:QU4 M235b 2009]
is_a: PW:0000642 ! fatty acid degradation pathway
created_by: VPetri
creation_date: 2010-02-17T03:06:21Z

[Term]
id: PW:0000741
name: altered ganglioside metabolic pathway
def: "A ganglioside metabolic pathway that deviates from what its normal course should be. For instance, Tay-Sachs disease is caused by a deficiency in the enzyme that degrades ganglioside GM2. This and other conditions involving impaired sphingolipid metabolism are collectively known as sphingolipid storage disease." [MCW library:QU4 M235b 2009]
is_a: PW:0000164 ! ganglioside metabolic pathway
is_a: PW:0000742 ! altered glycosphingolipid metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T12:39:44Z

[Term]
id: PW:0000742
name: altered glycosphingolipid metabolic pathway
def: "A glycoshingolipid metabolic pathway that deviates from what its normal course should be. Altered glycosphingolipid metabolism has been associated with several lysosomal storage diseases and most appear to be fatal." [MCW library:QU4 M235b 2009]
is_a: PW:0000733 ! glycosphingolipid metabolic pathway
is_a: PW:0000735 ! altered sphingolipid metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T01:03:56Z

[Term]
id: PW:0000743
name: galactocerebroside metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of galactocerebroside, a cerebroside in which the monosaccharide is galactose." [MCW library:QU4 M235b 2009]
is_a: PW:0000734 ! cerebroside metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T01:15:17Z

[Term]
id: PW:0000744
name: glucocerebroside metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glucocerebroside, a cerebroside in which the monosaccharide is glucose." [MCW library:QU4 M235b 2009]
is_a: PW:0000734 ! cerebroside metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T01:15:47Z

[Term]
id: PW:0000745
name: sphingomyelin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of sphingomyelin - a sphingolipid found abundantly in the myelin sheath of nerve cells." [GO:0006684, MCW library:QU4 M235b 2009]
is_a: PW:0000197 ! sphingolipid metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T01:28:17Z

[Term]
id: PW:0000746
name: altered sphingomyelin metabolic pathway
def: "A sphingomyelin metabolic pathway that deviates from what its normal course should be. For instance, Niemann-Pick disease is caused by a deficiency in the enzyme that degrades sphingomyelin. This and other conditions involving impaired sphingolipid metabolism are collectively known as sphingolipid storage disease." [MCW library:QU4 M235b 2009]
is_a: PW:0000735 ! altered sphingolipid metabolic pathway
is_a: PW:0000745 ! sphingomyelin metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T01:34:19Z

[Term]
id: PW:0000747
name: altered galactocerebroside metabolic pathway
def: "A galactocerebroside metabolic pathway that deviates from what its normal course should be. For instance, Krabbe's disease is caused by a deficiency in the enzyme that degrades galactocerebroside. This and other conditions involving impaired sphingolipid metabolism are collectively known as sphingolipid storage disease." [MCW library:QU4 M235b]
is_a: PW:0000743 ! galactocerebroside metabolic pathway
is_a: PW:0000748 ! altered cerebroside metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T01:41:25Z

[Term]
id: PW:0000748
name: altered cerebroside metabolic pathway
def: "A cerebroside metabolic pathway that deviates from what its normal course should be. Altered cerebroside metabolism has been associated with several lysosomal storage diseases and most appear to be fatal." [MCW library:QU4 M235b 2009]
is_a: PW:0000734 ! cerebroside metabolic pathway
is_a: PW:0000742 ! altered glycosphingolipid metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T01:45:45Z

[Term]
id: PW:0000749
name: altered glucocerebroside metabolic pathway
def: "A glucocerebroside metabolic pathway that deviates from what its normal course should be. For instance, Gaucher's disease is caused by a deficiency in the enzyme that degrades glucocerebroside. This and other conditions involving impaired sphingolipid metabolism are collectively known as sphingolipid storage disease." [MCW library:QU4 M235b 2009]
is_a: PW:0000744 ! glucocerebroside metabolic pathway
is_a: PW:0000748 ! altered cerebroside metabolic pathway
created_by: vpetri
creation_date: 2010-02-18T02:02:09Z

[Term]
id: PW:0000750
name: altered isoprenoid metabolic pathway
def: "An isoprenoid metabolic pathway that deviates from what its normal course should be. Aberrant isoprenoid metabolism, as evidenced in alterations in cholesterol metabolism, has been associated with a variety of conditions." [MCW library:QU85 B615 2008, PMID:16876788]
is_a: PW:0000248 ! isoprenoid metabolic pathway
is_a: PW:0000483 ! altered lipid metabolic pathway
created_by: VPetri
creation_date: 2010-02-23T03:06:26Z

[Term]
id: PW:0000751
name: altered isoprenoid biosynthetic pathway
def: "An isoprenoid biosynthetic pathway that deviates from what its normal course should be. Aberrant isoprenoid biosynthetic pathway, as evidenced in altered cholesterol biosynthesis has been associated with several conditions." [MCW library:QU85 B615 2008, PMID:16876788]
is_a: PW:0000453 ! isoprenoid biosynthetic pathway
is_a: PW:0000750 ! altered isoprenoid metabolic pathway
created_by: VPetri
creation_date: 2010-02-23T03:12:58Z

[Term]
id: PW:0000752
name: altered cholesterol biosynthetic pathway
def: "A cholesterol biosynthetic pathway that deviates from what its normal course should be. Aberrant cholesterol biosynthesis involves defects in enzymes of both early and later steps leading to several disorders." [MCW library:QU 85 B615 2008, PMID:16876788]
is_a: PW:0000454 ! cholesterol biosynthetic pathway
is_a: PW:0001306 ! altered steroid biosynthetic pathway
created_by: VPetri
creation_date: 2010-02-23T03:18:14Z

[Term]
id: PW:0000753
name: sterol regulatory element-binding protein signaling pathway
def: "The sterol regulatory element-binding protein (SREBP) pathway has important roles in the control of lipid and cholesterol metabolism. SREBPs are sterol regulated transcription factors that belong to the bHLH family." [PMID:17303406]
synonym: "SREBP signaling pathway" RELATED []
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
is_a: PW:0001371 ! basic helix-loop-helix signaling pathway
created_by: VPetri
creation_date: 2010-02-24T10:47:34Z

[Term]
id: PW:0000754
name: drug pathway
def: "The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs. The systems involved in drug processing and responses are also those handling exogenous, xenobiotic compounds in the cellular detoxification pathway. The distinction between a random encounter with a foreign compound and the processing of a substance administered for treatment along with the importance of genetic variation for the individual responses to particular drugs warrant their separate consideration." [KEGG:http\://www.genome.jp/kegg/, PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000001 ! pathway
created_by: VPetri
creation_date: 2010-03-15T11:01:15Z

[Term]
id: PW:0000755
name: benzodiazepine drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of benzodiazepines, a class of drugs acting upon the central nervous system. The drugs are administered as sedatives. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000923 ! nervous system drug pathway
created_by: VPetri
creation_date: 2010-03-15T11:26:01Z

[Term]
id: PW:0000756
name: benzodiazepine pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of benzodiazepines. Benzodiazepine represent a class of drugs used as sedatives. They act as ligands for the GABA-A receptor to stimulate its inhibitory activity. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000755 ! benzodiazepine drug pathway
created_by: VPetri
creation_date: 2010-03-15T11:30:00Z

[Term]
id: PW:0000757
name: benzodiazepine pharmacodynamics pathway
def: "The pathway of benzodiazepine-target interaction and of the biochemical or physiological responses to drug. Benzodiazepines are a class of drugs used as sedatives. They act as ligands for the GABA-A receptor to stimulate its inhibitory activity. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000755 ! benzodiazepine drug pathway
created_by: VPetri
creation_date: 2010-03-15T11:31:43Z

[Term]
id: PW:0000758
name: gemcitabine pathway
def: "The pharmacokinetics and pharmacodynamics pathway of gemcitabine, a cytidine analogue that is administered as a prodrug for the treatment of certain types of cancer. The diphosphate form is an inhibitor of ribonucleotide reductases, essential enzymes of deoxyribonucleotide synthesis. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2010-03-17T08:04:55Z

[Term]
id: PW:0000759
name: gemcitabine pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of gemcitabine. Gemcitabine is a cytidine analogue administered as a prodrug for the treatment of certain cancers. The diphosphate form is an inhibitor of ribonucleotide reductases, essential enzymes of deoxyribonucleotide synthesis. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA2036, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00446/pathway]
is_a: PW:0000758 ! gemcitabine pathway
created_by: VPetri
creation_date: 2010-03-17T08:18:10Z

[Term]
id: PW:0000760
name: gemcitabine pharmacodynamics pathway
def: "The pathway of gemcitabine-target interaction and of the biochemical or physiological responses to drug. Gemcitabine is a cytidine analogue that is administered as a prodrug for the treatment of certain types of cancer. The diphosphate form is an inhibitor of ribonucleotide reductases, essential enzymes of deoxyribonucleotide synthesis. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA2036, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00446/pathway]
is_a: PW:0000758 ! gemcitabine pathway
created_by: VPetri
creation_date: 2010-03-17T08:27:03Z

[Term]
id: PW:0000761
name: celecoxib drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of celecoxib, a selective cyclooxygenase 2 inhibitor used for the treatment of osteoarthritis and rheumatoid arthritis. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:www.pharmgkb.org/]
synonym: "celebrex pathway" RELATED []
is_a: PW:0001170 ! musculo-skeletal system drug pathway
created_by: VPetri
creation_date: 2010-03-17T08:51:56Z

[Term]
id: PW:0000762
name: celecoxib pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of celecoxib - a selective inhibitor of cyclooxygenase 2 used for the treatment of osteoarthritis and rheumatoid arthritis. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA152241951, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00096/pathway]
synonym: "celebrex pharmacokinetics pathway" RELATED []
is_a: PW:0000761 ! celecoxib drug pathway
created_by: VPetri
creation_date: 2010-03-17T09:03:48Z

[Term]
id: PW:0000763
name: celecoxib pharmacodynamics pathway
def: "The pathway of celecoxib-target interaction and of the biochemical or physiological responses to drug. Celecoxib is a selective inhibitor of cyclooxygenase 2 used for the treatment of osteoarthritis and rheumatoid arthritis. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA152241951, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00096/pathway]
is_a: PW:0000761 ! celecoxib drug pathway
created_by: VPetri
creation_date: 2010-03-17T09:14:56Z

[Term]
id: PW:0000764
name: ifosfamide drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of ifosfamide, am antitumor agent used in the treatment of certain cancers. It is administered as a prodrug that has to be converted to the active form. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00448/pathway]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2010-03-22T01:04:43Z

[Term]
id: PW:0000765
name: ifosfamide pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of ifosfamide, a prodrug used against solid tumors. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA2037, SMPFB:http\://pathman.smpdb.ca/pathways/SMP00448/pathway]
is_a: PW:0000764 ! ifosfamide drug pathway
created_by: VPetri
creation_date: 2010-03-22T01:13:38Z

[Term]
id: PW:0000766
name: ifosfamide pharmacodynamics pathway
def: "The pathway of ifosfamide-target interaction and of the biochemical or physiological responses to drug. Ifosfamide is administered as a prodrug and is widely used as an alkylating agent for the treatment of certain cancers. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/search/pathway/ifos/ifos-pd.jsp, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00448/pathway]
is_a: PW:0000764 ! ifosfamide drug pathway
created_by: VPetri
creation_date: 2010-03-22T01:21:34Z

[Term]
id: PW:0000767
name: omeprazole drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of omeprazole, a proton pump inhibitor. Omeprazole is the representative compound of a class of such inhibitors that are administered for the treatment of acid-related disorders. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00226/pathway]
synonym: "proton pump inhibitor pathway" RELATED []
is_a: PW:0000918 ! proton pump inhibitor drug pathway
created_by: VPetri
creation_date: 2010-03-22T01:39:19Z

[Term]
id: PW:0000768
name: omeprazole pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of omeprazole, a representative compound of a class of proton pump inhibitors. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA152530846, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00226/pathway]
synonym: "proton pump inhibitor pharmacokinetics pathway" RELATED []
is_a: PW:0000767 ! omeprazole drug pathway
created_by: VPetri
creation_date: 2010-03-22T01:44:57Z

[Term]
id: PW:0000769
name: omeprazole pharmacodynamics pathway
def: "The pathway of omeprazole-target interaction and of the biochemical or physiological responses to drug. Omeprazole is a representative compound of a class of proton pump inhibitors used in the treatment of acid-related disorders. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/search/pathway/proton-pump/proton-pump-pd.jsp, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00226/pathway]
synonym: "proton pump inhibitor pharmacodynamics pathway" RELATED []
is_a: PW:0000767 ! omeprazole drug pathway
created_by: VPetri
creation_date: 2010-03-22T01:50:32Z

[Term]
id: PW:0000770
name: C19-steroid hormone biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of C19-steroid hormones. Pregnenolone, a C21 steroid derived from cholesterol, and progesterone, to which pregnenolone can be converted, provide the starting material for the C21, C19 and C18 steroid hormones. The C19 class is represented by androgens such as testosterone." [PMID:17926129, PMID:18720009]
synonym: "androgen biosynthetic pathway" RELATED []
is_a: PW:0000040 ! steroid hormone biosynthetic pathway
created_by: VPetri
creation_date: 2010-04-20T03:43:21Z

[Term]
id: PW:0000771
name: mineralocorticoid biosynthetic pathway
def: "Mineralocorticoids are a group of C21 steroid hormones synthesized by the adrenal cortex and so named because of their effects on the concentration of sodium as well as potassium and chloride. The group is best exemplified by aldosterone." [OneLook:www.onelook.com]
is_a: PW:0000070 ! C21-steroid hormone biosynthetic pathway
created_by: VPetri
creation_date: 2010-04-20T04:01:52Z

[Term]
id: PW:0000772
name: glucocorticoid biosynthetic pathway
def: "Glucocorticoids are a group of C21 steroid hormones synthesized by the adrenal cortex and so named because of their effects on glucose metabolism. They also play a role in developmental processes and the immune system. The group is best exemplified by cortisol." [OneLook:www.onelook.com]
is_a: PW:0000070 ! C21-steroid hormone biosynthetic pathway
created_by: VPetri
creation_date: 2010-04-20T04:31:54Z

[Term]
id: PW:0000773
name: aldosterone biosynthetic pathway
def: "Aldosterone is a C21 mineralocorticoid produced in the outer zone, the zona glomerulosa, of the adrenal cortex from the cholesterol precursor. It plays important roles in the regulation of water and salt balance." [PMID:17926129]
is_a: PW:0000771 ! mineralocorticoid biosynthetic pathway
created_by: VPetri
creation_date: 2010-04-20T04:49:31Z

[Term]
id: PW:0000774
name: cortisol biosynthetic pathway
def: "Cortisol is a C21 glucocorticoid produced in the middle zone, the zona fasciculata, of the adrenal cortex from the cholesterol precursor. It plays important roles in carbohydrate and other nutrients metabolism." [PMID:17926129]
is_a: PW:0000772 ! glucocorticoid biosynthetic pathway
created_by: VPetri
creation_date: 2010-04-20T04:49:53Z

[Term]
id: PW:0000775
name: altered epidermal growth factor/neuregulin signaling pathway
def: "An epidermal growth factor/neuregulin signaling pathway that deviates from what its normal course should be. Deregulation of the pathway, mostly as upregulation due to the increased expression or amplification of ligands and/or receptors, or mutations leading to such increases, has been linked to numerous forms of cancer, such as pancreatic, lung, endometrial and breast." [InHouse:PW dictionary]
is_a: PW:0000170 ! epidermal growth factor/neuregulin signaling pathway
is_a: PW:0000298 ! altered growth factor signaling pathway
created_by: VPetri
creation_date: 2010-04-26T10:53:15Z

[Term]
id: PW:0000776
name: ketone bodies biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of acetoacetate and beta-hydroxybutyrate also known as ketone bodies although only acetoacetate is a ketone. Generally, the acetyl-CoA derived from fatty acids oxidation enters the citrate cycle. In the liver, a substantial fraction of acetyl-CoA is converted to ketone bodies which are then released into the blood stream for supply to peripheral tissues." [GO:0042181, KEGG:map00072, MCW Libraries:QU4 V876f 2008, Reactome:REACT_1464.3]
is_a: PW:0000069 ! ketone bodies metabolic pathway
created_by: VPetri
creation_date: 2010-05-20T01:06:48Z

[Term]
id: PW:0000777
name: ketone bodies degradation pathway
def: "Those metabolic reactions that convert acetoacetate and beta-hydroxybutyrate back to acetyl-CoA which then can enter the citrate cycle for energy production. The ketone bodies are synthesized in the liver and released into to blood stream to supply fuel to peripheral tissues, heart and skeletal muscle in particular and during starvation, the brain." [GO:0046952, KEGG:map00072, MCW Libraries:QU4 V876f 2008]
is_a: PW:0000069 ! ketone bodies metabolic pathway
created_by: VPetri
creation_date: 2010-05-20T01:23:02Z

[Term]
id: PW:0000778
name: testosterone biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of testosterone, a C19-steroid hormone secreted primarily in the testes and ovaries and to a lesser extend by the adrenal glands." [OneLook:www.onelook.com]
is_a: PW:0000770 ! C19-steroid hormone biosynthetic pathway
created_by: VPetri
creation_date: 2010-05-20T02:21:52Z

[Term]
id: PW:0000779
name: dehydroepiandrosterone biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of dehydroepiandrosterone, a C19 steroid hormone produced in the adrenal cortex and a primary precursor of estrogens." [OneLook:www.onelook.com]
synonym: "DHEA biosynthetic pathway" RELATED []
is_a: PW:0000770 ! C19-steroid hormone biosynthetic pathway
created_by: VPetri
creation_date: 2010-05-20T02:25:04Z

[Term]
id: PW:0000780
name: C18-steroid hormone biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of C18-steroid hormones. Pregnenolone, a C21 steroid derived from cholesterol, and progesterone, to which pregnenolone can be converted, provide the starting material for the C21, C19 and C18 steroid hormones. The C18 class is represented by estrogens. The major natural estrogens are beta-estradiol - the primary estrogen, the estrone of menopause and the estriol of pregnancy." [OneLook:www.onelook.com, PMID:17926129]
synonym: "estrogen biosynthetic pathway" RELATED []
is_a: PW:0000040 ! steroid hormone biosynthetic pathway
created_by: VPetri
creation_date: 2010-05-20T02:42:49Z

[Term]
id: PW:0000781
name: estradiol biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of estradiol, the major C18 steroid hormone. The term generally refers to the 17 beta isomer, the most potent form of estrogen." [OneLook:www.onelook.com]
synonym: "17beta-estradiol biosynthetic pathway" RELATED []
is_a: PW:0000780 ! C18-steroid hormone biosynthetic pathway
created_by: VPetri
creation_date: 2010-05-20T03:08:05Z

[Term]
id: PW:0000782
name: glucocorticoid signaling pathway
def: "Glucocorticoids, C21-steroid hormones, initiate signaling by binding to their specific nuclear receptor to regulate metabolism, development and immune response. The major glucocorticoid is cortisol." [OneLook:www.onelook.com]
is_a: PW:0000566 ! corticosteroid signaling pathway
created_by: VPetri
creation_date: 2010-05-21T01:43:39Z

[Term]
id: PW:0000783
name: mineralocorticoid signaling pathway
def: "Mineralocorticoids, C21 steroid hormones, initiate signaling by binding to their cognate receptor to regulate water and mineral levels. The main endogenous mineralocorticoid is aldosterone." [OneLook:www.onelook.com]
is_a: PW:0000566 ! corticosteroid signaling pathway
created_by: VPetri
creation_date: 2010-05-21T02:05:00Z

[Term]
id: PW:0000784
name: altered androgen signaling pathway
def: "An androgen signaling pathway that deviates from what its normal course should be. Altered androgen signaling, due to upregulation of the androgen receptor, has been implicated in prostate cancer." [PMID:17163421, PMID:18657355]
is_a: PW:0000564 ! androgen signaling pathway
is_a: PW:0000719 ! altered transcription factor mediated signaling pathway
is_a: PW:0000787 ! altered sex steroids signaling pathway
is_a: PW:0001314 ! altered transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2010-06-01T09:36:38Z

[Term]
id: PW:0000785
name: altered lipid hormone signaling pathway
is_a: PW:0000469 ! lipid hormone signaling pathway
is_a: PW:0000509 ! altered hormone signaling pathway
created_by: VPetri
creation_date: 2010-06-02T09:54:05Z

[Term]
id: PW:0000786
name: altered steroid hormone signaling pathway
is_a: PW:0000468 ! steroid hormone signaling pathway
is_a: PW:0000785 ! altered lipid hormone signaling pathway
created_by: VPetri
creation_date: 2010-06-02T09:54:34Z

[Term]
id: PW:0000787
name: altered sex steroids signaling pathway
is_a: PW:0000567 ! sex steroids signaling pathway
is_a: PW:0000786 ! altered steroid hormone signaling pathway
created_by: VPetri
creation_date: 2010-06-02T09:55:15Z

[Term]
id: PW:0000788
name: glucose-dependent insulinotropic peptide signaling pathway
def: "Glucose-dependent insulinotropic peptide signaling plays an important role in promoting insulin secretion. Gip is secreted from the K intestinal cells in response to nutrient ingestion. It signals via a G-protein coupled receptor to increase calcium and cAMP and activate downstream signaling pathways." [PMID:19074620]
synonym: "GIP signaling pathway" RELATED []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2010-06-18T02:32:43Z

[Term]
id: PW:0000789
name: glucagon-like peptide-1 signaling pathway
def: "Glucagon-like peptide-1 signaling pathway plays an important role in promoting insulin secretion. GLp-1 is secreted from the L intestinal cells in response to nutrient ingestion. It signals via a G-protein coupled receptor to increase calcium and cAMP and activate numerous downstream signaling pathways." [PMID:19074620]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2010-06-18T02:44:07Z

[Term]
id: PW:0000790
name: epinephrine signaling pathway
def: "Epinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha receptor 1 and 2 couple to the Galphaq and Galphai subunits of heterotrimeric G proteins, respectively. The three beta receptors couple to the Galphas subunit." [OneLook:www.onelook.com]
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse
is_a: PW:0000798 ! catecholamine signaling pathway
created_by: VPetri
creation_date: 2010-06-18T03:39:46Z

[Term]
id: PW:0000791
name: norepinephrine signaling pathway
def: "Norepinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha receptor 1 and 2 couple to the Galphaq and Galphai subunits of heterotrimeric G proteins, respectively. The three beta receptors couple to the Galphas subunit." [OneLook:www.onelook.com]
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse
is_a: PW:0000798 ! catecholamine signaling pathway
created_by: VPetri
creation_date: 2010-06-18T03:50:51Z

[Term]
id: PW:0000792
name: epinephrine signaling pathway via adrenergic receptor alpha 1
def: "Epinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha 1 receptors couple to the Galphaq subunit." [OneLook:www.onelook.com]
is_a: PW:0000790 ! epinephrine signaling pathway
created_by: VPetri
creation_date: 2010-06-18T03:54:56Z

[Term]
id: PW:0000793
name: epinephrine signaling pathway via adrenergic receptor alpha 2
def: "Epinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha 2 receptors couple to the Galphai subunit." [OneLook:www.onelook.com]
is_a: PW:0000790 ! epinephrine signaling pathway
created_by: VPetri
creation_date: 2010-06-18T03:55:32Z

[Term]
id: PW:0000794
name: epinephrine signaling pathway via adrenergic receptor beta
def: "Epinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The beta receptors couple to the Galphas subunit. Beta 2 receptor may also couple to Galphai." [OneLook:www.onelook.com]
is_a: PW:0000790 ! epinephrine signaling pathway
created_by: VPetri
creation_date: 2010-06-18T03:56:07Z

[Term]
id: PW:0000795
name: norepinephrine signaling pathway via adrenergic receptor alpha 1
def: "Norepinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha 1 receptors couple to the Galphaq subunit." [OneLook:www.onelook.com]
is_a: PW:0000791 ! norepinephrine signaling pathway
created_by: VPetri
creation_date: 2010-06-18T03:58:19Z

[Term]
id: PW:0000796
name: norepinephrine signaling pathway via adrenergic receptor alpha 2
def: "Norepinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha 2 receptors couple to the Galphai subunit." [OneLook:www.onelook.com]
is_a: PW:0000791 ! norepinephrine signaling pathway
created_by: VPetri
creation_date: 2010-06-18T03:59:08Z

[Term]
id: PW:0000797
name: norepinephrine signaling pathway via adrenergic receptor beta
def: "Norepinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The beta receptors couple to the Galphas subunit. Beta 2 receptor may also couple to Galphai." [OneLook:www.onelook.com]
is_a: PW:0000791 ! norepinephrine signaling pathway
created_by: VPetri
creation_date: 2010-06-18T03:59:44Z

[Term]
id: PW:0000798
name: catecholamine signaling pathway
def: "Catecholamines act as hormones and neurotransmitters. The major catecholamines are dopamine, epinephrine and norepinephrine. They are derived from tyrosine and are not to be confused with tyrosine-based hormones." [OneLook:www.onelook.com]
is_a: PW:0000466 ! amine and amino acid-derived hormone signaling pathway
created_by: VPetri
creation_date: 2010-06-18T04:09:20Z

[Term]
id: PW:0000799
name: adrenergic beta receptor drug pathway - beta-agonist and beta-blocker
def: "The pharmacokinetics and pharmacodynamics pathway of adrenergic beta receptors drugs - beta-agonists and blockers. Adrenergic beta receptors, in response to epinephrine or norepinephrine couple to the Gs alpha subunit of heterotrimeric G protein to elicit several responses. Beta-agonists are used to stimulate while beta-blocker antagonists are used to inhibit these responses, as necessary. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:19874988]
is_a: PW:0000920 ! cardiovascular system drug pathway
is_a: PW:0000924 ! respiratory system drug pathway
created_by: VPetri
creation_date: 2010-06-30T10:47:27Z

[Term]
id: PW:0000800
name: adrenergic beta receptor agonist and beta-blocker pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of beta adrenergic receptor drugs. The beta-agonists are used to stimulate while the beta-blockers are used to inhibit the action of adrenergic beta receptors, as necessary. Adrenergic beta receptors are G-protein coupled receptors that in response to epinephrine or norepinephrine elicit various sympathetic responses important for proper cardiac function and in the case of beta2 receptor, smooth muscle relaxation and bronchodilation. Genetic variations can result in changes in the availability of the drug." [PMID:19874988]
is_a: PW:0000799 ! adrenergic beta receptor drug pathway - beta-agonist and beta-blocker
created_by: VPetri
creation_date: 2010-07-01T08:56:44Z

[Term]
id: PW:0000801
name: adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway
def: "The pathway of beta adrenergic drug-target interactions and of the biochemical or physiological responses to them. The beta-agonists are used to stimulate while the beta-blockers are used to inhibit the action of adrenergic beta receptors, as necessary. Adrenergic beta receptors are G-protein coupled receptors that in response to epinephrine or norepinephrine elicit various sympathetic responses important for proper cardiac function and in the case of beta2 receptor, smooth muscle relaxation and bronchodilation. Genetic variations can cause differences in the response of the organism to the drug." [PMID:19874988]
is_a: PW:0000799 ! adrenergic beta receptor drug pathway - beta-agonist and beta-blocker
created_by: VPetri
creation_date: 2010-07-01T09:12:37Z

[Term]
id: PW:0000802
name: dopamine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of dopamine." [PMID:19342614]
is_a: PW:0000409 ! dopamine metabolic pathway
is_a: PW:0001235 ! catecholamine biosynthetic pathway
created_by: VPetri
creation_date: 2010-08-13T02:17:38Z

[Term]
id: PW:0000803
name: epinephrine biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of epinephrine. Epinephrine is primarily synthesized in adrenal chromaffin cells in response to specific stresses that activate the sympatho-adreno-medullary system." [PMID:19342614]
is_a: PW:0000441 ! epinephrine metabolic pathway
is_a: PW:0001235 ! catecholamine biosynthetic pathway
created_by: VPetri
creation_date: 2010-08-13T02:18:06Z

[Term]
id: PW:0000804
name: norepinephrine biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of norepinephrine. Norepinephrine is primarily synthesized in sympathetic neurons in response to stresses such as cold or pain." [PMID:19342614]
is_a: PW:0000442 ! norepinephrine metabolic pathway
is_a: PW:0001235 ! catecholamine biosynthetic pathway
created_by: VPetri
creation_date: 2010-08-13T02:18:28Z

[Term]
id: PW:0000805
name: altered Trail mediated signaling pathway
def: "A Trail mediated signaling pathway that deviates from what its normal course should be. Mutations with the death domain of the receptors or deletions within the region containing the receptor genes have been reported for certain types of lymphomas." [PMID:18813321, PMID:20336667]
is_a: PW:0000680 ! altered extrinsic apoptotic pathway
is_a: PW:0000682 ! Trail mediated signaling pathway
created_by: VPetri
creation_date: 2010-09-10T04:41:18Z

[Term]
id: PW:0000806
name: altered FasL mediated signaling pathway
def: "A FasL mediated signaling pathway that deviates from what its normal course should be." [PMID:10712254]
is_a: PW:0000680 ! altered extrinsic apoptotic pathway
is_a: PW:0000681 ! FasL mediated signaling pathway
created_by: VPetri
creation_date: 2010-09-10T05:12:24Z

[Term]
id: PW:0000807
name: altered transcription pathway
def: "A transcription pathway that deviates from what its normal course should be. Aberrant transcription can have devastating consequences. Altered signaling mediated by various transcription factors has been implicated in a spectrum of human diseases." [InHouse:InHouse PW dictionary]
is_a: PW:0000100 ! transcription pathway
is_a: PW:0000290 ! altered pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
created_by: VPetri
creation_date: 2010-10-08T11:40:35Z

[Term]
id: PW:0000808
name: microRNA pathway
def: "MicroRNAs (miRNAs) are a large family of small RNAs involved in the post transcriptional regulation of gene expression. The biogenesis and function of miRNA is subject to complex control. Deregulation of miRNA expression has been linked to many diseases including cancer." [PMID:20471939, PMID:20661255, PMID:20885409]
synonym: "miRNA pathway" RELATED []
is_a: PW:0000809 ! small non-coding RNA pathway
created_by: VPetri
creation_date: 2010-10-08T12:35:16Z

[Term]
id: PW:0000809
name: small non-coding RNA pathway
def: "The small non-coding RNA pathways have emerged as potent regulators of gene expression. Three major classes have been identified of which the microRNA (miRNA) system is the better understood one." [PMID:19165215, PMID:20484662]
is_a: PW:0001334 ! non-coding RNA pathway
created_by: VPetri
creation_date: 2010-10-15T02:16:18Z

[Term]
id: PW:0000810
name: endogenous small interfering RNA pathway
synonym: "endo-siRNA" RELATED []
is_a: PW:0000809 ! small non-coding RNA pathway
created_by: VPetri
creation_date: 2010-10-15T03:37:08Z

[Term]
id: PW:0000811
name: Piwi-interacting RNA pathway
def: "Piwi-RNA (piRNAs) are believed to play a role in gene silencing, particularly the silencing of transposons as many" [Cell:new article]
synonym: "piRNA pathway" RELATED []
is_a: PW:0000809 ! small non-coding RNA pathway
created_by: VPetri
creation_date: 2010-10-15T03:48:40Z

[Term]
id: PW:0000812
name: altered small non-coding RNA pathway
def: "A small non-coding RNA pathway that deviates from what its normal course should. For instance, alterations in miRNA pathway have been associated with many diseases including various types of cancer." [PMID:19882673, PMID:20885409]
is_a: PW:0000290 ! altered pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
is_a: PW:0000809 ! small non-coding RNA pathway
created_by: VPetri
creation_date: 2010-10-15T03:53:29Z

[Term]
id: PW:0000813
name: altered microRNA pathway
def: "A microRNA pathway that deviates from what its normal course should be. An altered miRNA pathway has been implicated in many diseases including various forms of cancer." [PMID:20885409]
synonym: "altered miRNA pathway" RELATED []
is_a: PW:0000808 ! microRNA pathway
is_a: PW:0000812 ! altered small non-coding RNA pathway
created_by: VPetri
creation_date: 2010-10-15T04:05:12Z

[Term]
id: PW:0000814
name: Toll-like receptor signaling pathway
def: "Toll-like receptors represent a large and the better understood family of pattern recognition receptors that sense an array of exogenous structures and recent evidence shows they can also recognize defective endogenous molecules. The intracellular signaling cascades they set in motion lead to the expression of inflammatory mediators." [PMID:20303867, PMID:20303872]
synonym: "KEGG:04620" RELATED []
synonym: "TLR signaling pathway" EXACT []
is_a: PW:0000925 ! pattern recognition receptor mediated signaling pathway
created_by: VPetri
creation_date: 2010-10-27T11:29:27Z

[Term]
id: PW:0000815
name: C-type lectin receptor signaling pathway
def: "C-type lectin receptors represent one of four classes of pattern recognition receptors. The intracellular signaling cascades they set in motion lead to the expression of inflammatory mediators." [PMID:20303867, PMID:20303872]
is_a: PW:0000925 ! pattern recognition receptor mediated signaling pathway
created_by: VPetri
creation_date: 2010-10-27T11:38:01Z

[Term]
id: PW:0000816
name: Retinoic acid-inducible gene (RIG) I-like receptor signaling pathway
def: "This family of pattern recognition receptors are cytoplasmic proteins that recognize exogenous cytoplasmic DNA. The signaling cascades they set in motion lead to the expression of inflammatory mediators." [PMID:20303867, PMID:20303872]
synonym: "KEGG:04622" RELATED []
synonym: "RLR signaling pathway" EXACT []
is_a: PW:0000925 ! pattern recognition receptor mediated signaling pathway
created_by: VPetri
creation_date: 2010-10-27T11:43:26Z

[Term]
id: PW:0000817
name: NOD-like receptor signaling pathway
def: "NOD-like receptors are cytosolic proteins that recognize components of bacterial peptidoglycans. The signaling cascades they set in motion lead to the expression of inflammatory mediators." [PMID:20303867, PMID:20303872]
synonym: "KEGG:04621" RELATED []
synonym: "NLR signaling pathway" EXACT []
is_a: PW:0000925 ! pattern recognition receptor mediated signaling pathway
created_by: VPetri
creation_date: 2010-10-27T11:45:03Z

[Term]
id: PW:0000818
name: signaling pathway pertinent to immunity
def: "Those signaling pathways that are involved in or mediate the various aspects of immune responses." [MCW library:Cellular and molecular immunity\, by Abbas\, Abul K]
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2010-10-27T03:08:21Z

[Term]
id: PW:0000819
name: signaling pathway in the innate immune response
is_a: PW:0000818 ! signaling pathway pertinent to immunity
created_by: VPetri
creation_date: 2010-10-27T03:09:00Z

[Term]
id: PW:0000820
name: signaling pathway in the adaptive immune response
is_a: PW:0000818 ! signaling pathway pertinent to immunity
created_by: VPetri
creation_date: 2010-10-27T03:09:29Z

[Term]
id: PW:0000821
name: T cell receptor signaling pathway
def: "T cell receptor (TCR) signaling in developing thymocytes is important for the establishment of CD4 and CD8 lineages. Mature T cells express either CD4 or CD8 co-receptors which are essential for the interaction with peptide-bound class II or class I MHC complexes to elicit CD4 T helper (Th) or CD8 cytotoxic T lymphocyte responses, respectively. In either case, T cells initiated signaling activates the expression of genes whose products mediate these responses." [MCW library:Handbook of cellular and molecular immunology, PMID:16448548, PMID:20537906]
synonym: "KEGG:04660" RELATED []
synonym: "TCR signaling pathway" EXACT []
is_a: PW:0000820 ! signaling pathway in the adaptive immune response
relationship: part_of PW:0000824 ! cell-mediated immunity pathway
created_by: VPetri
creation_date: 2010-10-27T03:28:43Z

[Term]
id: PW:0000822
name: B cell receptor signaling pathway
def: "Antigen recognition by B cell receptors initiates signaling cascades that activate the expression of genes whose products are important for B cell functional responses." [MCW library:Handbook on cellular and molecular immunology, PMID:19827951, PMID:20591989]
synonym: "BCR signaling pathway" EXACT []
synonym: "KEGG:04662" RELATED []
is_a: PW:0000820 ! signaling pathway in the adaptive immune response
relationship: part_of PW:0000823 ! humoral immunity pathway
created_by: VPetri
creation_date: 2010-10-27T04:44:51Z

[Term]
id: PW:0000823
name: humoral immunity pathway
def: "Humoral immunity is mediated by antibodies secreted by the B cell lymphocytes. Antibodies recognize antigens of extracellular microbes and act to neutralize and eliminate them. Activation of B cells can occur in a T cell dependent or independent manner." [MCW library:Textbook on cellular and molecular immunology]
is_a: PW:0000235 ! adaptive immune response pathway
created_by: VPetri
creation_date: 2010-11-01T01:49:11Z

[Term]
id: PW:0000824
name: cell-mediated immunity pathway
def: "Cell-mediated immune response pathways are carried out by T cell lymphocytes. T cells receptors recognize peptides bound to a major histocompatibility complex (MHC) on the antigen presenting cell. Depending on whether the co-receptor is CD4 or CD8, the receptors will interact with MHC class II or class I to elicit distinct responses against intracellular pathogens." [MCW library:Handbook of cellular and molecular immunology]
is_a: PW:0000235 ! adaptive immune response pathway
created_by: VPetri
creation_date: 2010-11-01T01:49:42Z

[Term]
id: PW:0000825
name: antigen processing and presentation pathway
def: "The pathways of antigen processing and presentation assure the generation of peptides that have the structural attributes necessary for the association with and their placement near major histocompatibility complex (MHC) molecules. Protein antigen present in vesicular compartments generate class II peptides, those in cytosol class I." [MCW library:Handbook on cellular and molecular immunology]
synonym: "KEGG:04612" RELATED []
relationship: part_of PW:0000824 ! cell-mediated immunity pathway
created_by: VPetri
creation_date: 2010-11-01T05:17:15Z

[Term]
id: PW:0000826
name: T cell receptor signaling pathway in CD4+ T cells
def: "T cells that express the CD4 co-receptor, also called T helper cells, recognize class II MHC presented antigens derived from internalized microbes to initiate a signaling cascade that results in enhanced microbicidal capacity of phagocytes. T helper cells can be further subdivided into subsets of CD4+ T cells based on the distinct cytokines they produce and effector functions they perform." [MCW:Handbook on cellular and molecular immunology]
is_a: PW:0000821 ! T cell receptor signaling pathway
created_by: VPetri
creation_date: 2010-11-03T10:24:41Z

[Term]
id: PW:0000827
name: T cell receptor signaling pathway in CD8+ T cells
def: "T cells that express the CD8 co-receptor, also called cytotoxic or cytolytic T cells, recognize class I MHC presented antigens derived from cytosolic proteins to initiate a signaling cascade that results in killing of the target cell." [MCW:Handbook on cellular and molecular immunology]
is_a: PW:0000821 ! T cell receptor signaling pathway
created_by: VPetri
creation_date: 2010-11-03T10:44:22Z

[Term]
id: PW:0000828
name: cytokine mediated signaling pathway
def: "Cytokine initiated signaling pathways play important roles in innate and adaptive immunity, as well as cell proliferation and apoptosis." [MCW library:Handbook on molecular and cellular immunology]
synonym: "KEGG:04060" RELATED []
is_a: PW:0000577 ! cytokine and chemokine mediated signaling pathway
is_a: PW:0000818 ! signaling pathway pertinent to immunity
created_by: VPetri
creation_date: 2010-11-03T03:48:57Z

[Term]
id: PW:0000829
name: chemokine mediated signaling pathway
def: "Chemokine initiated pathways play important roles in the innate and adaptive immunity. They are also involved in development and tissue maintenance. The presence and localization of four cysteines is important for structural folding and is also the basis for chemokine classification. The spacing between the first two cysteine residues divides the family members into four groups. Most mammalian chemokines belong to the CC and CXC families. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW library:Handbook on molecular and cellular immunology, PMID:15062643]
synonym: "KEGG:04062" RELATED []
is_a: PW:0000577 ! cytokine and chemokine mediated signaling pathway
is_a: PW:0000818 ! signaling pathway pertinent to immunity
created_by: VPetri
creation_date: 2010-11-03T04:27:00Z

[Term]
id: PW:0000830
name: CXC chemokine mediated signaling pathway
def: "The CXC family members are characterized by the presence of two cysteine resides separated by one amino acid. CXC and CC are the two most prominent families. This family of chemokines is also subdivided into two subgroups: the one with the ELR motif - ELR (+) and the one without - ELR(-), respectively. Generally, ELR(+) and ELR(-) members bind to distinct chemokine, G-coupled protein, receptors. The effects of their signaling is for the most part angiogenic or angiostatic, respectively." [MCW:Handbook on cellular and molecular immunology, PMID:15062643, PMID:18579287]
is_a: PW:0000829 ! chemokine mediated signaling pathway
created_by: VPetri
creation_date: 2010-11-04T11:30:26Z

[Term]
id: PW:0000831
name: CC chemokine mediated signaling pathway
def: "The CC family members are characterized by the presence of two adjacent cysteine residues. The CC and the CXC family are the two most prominent families. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW:Handbook on cellular and molecular biology]
is_a: PW:0000829 ! chemokine mediated signaling pathway
created_by: VPetri
creation_date: 2010-11-04T11:30:33Z

[Term]
id: PW:0000832
name: C chemokine mediated signaling pathway
def: "The C family of chemokine is small and its members have two rather than four cysteines residues. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW:Handbook on cellular and molecular immunology, PMID:15062643]
is_a: PW:0000829 ! chemokine mediated signaling pathway
created_by: VPetri
creation_date: 2010-11-04T11:32:38Z

[Term]
id: PW:0000833
name: CX3C chemokine mediated signaling pathway
def: "The CX3X family of chemokine is small and characterized by the presence of three residues separating the first two cysteines. Currently, only one member is known in mammals. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW:Handbook on cellular and molecular immunology, PMID:15062643]
is_a: PW:0000829 ! chemokine mediated signaling pathway
created_by: VPetri
creation_date: 2010-11-12T05:03:05Z

[Term]
id: PW:0000834
name: bile acid transport pathway
def: "Bile acid absorption by the intestinal epithelium and hepatic recycling collectively group the transport pathway of the important molecules of cholesterol catabolism." [PMID:17404808, PMID:18837078]
synonym: "KEGG:04976" RELATED []
is_a: PW:0000103 ! transport pathway
created_by: VPetri
creation_date: 2010-12-22T02:05:33Z

[Term]
id: PW:0000835
name: anti-estrogen drug pathway
def: "Breast cancer is a major cause of death among Western women and many breast tumors are estrogen-dependent. Pharmacologically two major therapies have been developed: one targets the estrogen receptors via antagonists and selective modulators (SERM) and the second targets estrogen synthesis via aromatase inhibitors." [PMID:20644568]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2011-01-06T02:11:32Z

[Term]
id: PW:0000836
name: aromatase inhibitor pathway
def: "Aromatase inhibitors block the last step of estrogen biosynthesis. They can be classified into first-, second- and third-generation drugs. Depending on whether they inactivate the aromatase complex irreversibly or reversibly, they can be further subdivided into type I and II, respectively. Currently, third generation drugs are being used." [PMID:12402060, PMID:14513434]
is_a: PW:0000835 ! anti-estrogen drug pathway
created_by: VPetri
creation_date: 2011-01-07T05:07:46Z

[Term]
id: PW:0000837
name: tamoxifen drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of tamoxifen - one of the most widely used anti-estrogen drug that targets the estrogen receptor. The drug is a modulator than acts as an antagonist in breast cancer cells but can be an agonist in bone and the cardiovascular system. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:19629072]
is_a: PW:0000835 ! anti-estrogen drug pathway
created_by: VPetri
creation_date: 2011-01-17T01:05:40Z

[Term]
id: PW:0000838
name: tamoxifen pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of tamoxifen - a SERM anti-estrogen drug. Genetic variations can result in changes in the availability of the drug. For instance, variation in CYP2D6, an important enzyme for the production of a primary drug metabolite, impacts on the available concentration of the drug." [PMID:19629072]
is_a: PW:0000837 ! tamoxifen drug pathway
created_by: VPetri
creation_date: 2011-01-17T01:06:28Z

[Term]
id: PW:0000839
name: tamoxifen pharmacodynamics pathway
def: "The pathway of tamoxifen-target interaction and of the biochemical or physiological responses to it. In breast cancer cells, tamoxifen binding antagonizes estrogen binding and the subsequent conformational changes necessary for co-activators recruitment. It may also prompt the recruitment of co-repressor. Genetic variations can cause differences in the response of the organism to the drug." [PMID:19629072]
is_a: PW:0000837 ! tamoxifen drug pathway
created_by: VPetri
creation_date: 2011-01-17T01:06:59Z

[Term]
id: PW:0000840
name: protein kinase C (PKC) signaling pathway
def: "Protein kinase C constitutes a family of serine/threonine kinases activated by diacylglycerol (DAG) and calcium whose signal transduction plays important roles in many cellular processes. Ligand activated G protein-coupled receptors, via Galphaq pathway, stimulate phospholipase C which cleaves PIP2 into DAG and IP3. IP3 promotes calcium release." [GO:0070528, PMID:19934406]
is_a: PW:0000541 ! signaling pathway involving second messengers
is_a: PW:0001194 ! serine/threonine-specific kinase mediated signaling pathway
created_by: VPetri
creation_date: 2011-03-09T10:02:32Z

[Term]
id: PW:0000841
name: acetylcholine signaling pathway
def: "Acetylcholine signaling plays important roles in the central and peripheral nervous system and exerts both excitatory and inhibitory effects." [OneLook:www.onelook.com]
synonym: "ACh signaling pathway" EXACT []
synonym: "KEGG:04725" RELATED []
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse
created_by: VPetri
creation_date: 2011-03-09T11:08:00Z

[Term]
id: PW:0000842
name: acetylcholine signaling pathway via nicotinic acetylcholine receptor
def: "Activation of ionotropic nicotinic acetylcholine receptor leads to membrane depolarization and subsequent excitatory postsynaptic potential and to activation of voltage-gated ion channels. In humans, 17 subunits have been identified that can form various pentameric receptors." [OneLook:www.onelook.com]
is_a: PW:0000841 ! acetylcholine signaling pathway
created_by: VPetri
creation_date: 2011-03-09T11:18:32Z

[Term]
id: PW:0000843
name: acetylcholine signaling pathway via muscarinic acetylcholine receptor
def: "Acetylcholine signaling via the metabotropic muscarinic receptors exerts important roles in the parasympathetic nervous system. The five G protein-coupled receptors can be classified according to the G proteins they engage. Receptors M1, M3 and M5 predominantly couple to Galphaq whereas receptors M2 and M4 predominantly coupled to Galphai pathways." [GO:0007213, OneLook:www.onelook.com, PMID:18082893]
is_a: PW:0000841 ! acetylcholine signaling pathway
created_by: VPetri
creation_date: 2011-03-09T11:29:22Z

[Term]
id: PW:0000844
name: glutamate signaling pathway
def: "Glutamate signaling via the ionotropic AMPA or NMDA and several metabotropic receptors plays important roles in the modulation of synaptic plasticity, long term depression or potentiation, and in learning and memory." [GO:0007215, OneLook:www.onelook.com]
synonym: "KEGG:04724" RELATED []
is_a: PW:0000455 ! excitatory synaptic transmission pathway
created_by: VPetri
creation_date: 2011-03-09T11:57:08Z

[Term]
id: PW:0000845
name: glutamate signaling pathway via NMDA receptor
def: "Glutamate signaling via the ionotropic NMDA glutamate receptor plays important roles in synaptic plasticity and in learning and memory. The receptor is ligand-gated and voltage-dependent and requires glycine as a co-agonist." [GO:0035235, OneLook:www.onelook.com]
is_a: PW:0000844 ! glutamate signaling pathway
created_by: VPetri
creation_date: 2011-03-09T12:10:19Z

[Term]
id: PW:0000846
name: glutamate signaling pathway via AMPA receptor
def: "Glutamate signaling via the ionotropic AMPA receptor plays important roles in long-term potentiation (LTP). The AMPA receptors are both receptors and cation channels." [GO:0035235, OneLook:www.onelook.com]
is_a: PW:0000844 ! glutamate signaling pathway
created_by: VPetri
creation_date: 2011-03-09T12:24:02Z

[Term]
id: PW:0000847
name: glutamate signaling pathway via metabotropic glutamate receptor
def: "Glutamate signaling via the various metabotropic, G protein-coupled receptors plays important roles in both the central and peripheral nervous systems. Based on their structure and physiological function, the receptors have been classified into three groups. Group I receptors couple to Galphaq, group II and III couple to Galphai" [GO:0007216, OneLook:www.onelook.com]
is_a: PW:0000844 ! glutamate signaling pathway
created_by: VPetri
creation_date: 2011-03-09T01:06:26Z

[Term]
id: PW:0000848
name: gamma-aminobutyric acid signaling pathway
def: "Gamma-aminobutyric acid signals at inhibitory synapses via the type A receptor, which is part of a ligand-gated ion channel and the type B receptors which are metabotropic, G protein-coupled receptors." [GO:0007214, OneLook:www.onelook.com]
synonym: "KEGG:04727" RELATED []
is_a: PW:0000456 ! Inhibitory synaptic transmission pathway
created_by: VPetri
creation_date: 2011-03-09T02:10:16Z

[Term]
id: PW:0000849
name: glutamate signaling pathway via group I metabotropic glutamate receptor
is_a: PW:0000847 ! glutamate signaling pathway via metabotropic glutamate receptor
created_by: VPetri
creation_date: 2011-03-09T03:02:04Z

[Term]
id: PW:0000850
name: glutamate signaling pathway via group II or III glutamate receptor
is_a: PW:0000847 ! glutamate signaling pathway via metabotropic glutamate receptor
created_by: VPetri
creation_date: 2011-03-09T03:03:07Z

[Term]
id: PW:0000851
name: dopamine signaling pathway via D1 family of receptors
def: "Dopamine signaling via D1-like receptors engages the Galphas family of G proteins leading to activation of adenylyl cyclases and increase in intracellular cAMP. Dopamine receptors 1 and 5 belong to this family." [GO:0007212, OneLook:www.onelook.com, PMID:17413183]
is_a: PW:0000394 ! dopamine signaling pathway
created_by: VPetri
creation_date: 2011-03-09T03:15:01Z

[Term]
id: PW:0000852
name: dopamine signaling pathway via D2 family of receptors
def: "Dopamine signaling via D2-like family of receptors engages the Galphai family of G proteins leading to inhibition of adenylyl cyclases and reduction of intracellular cAMP. Dopamine receptors 2, 3 and 4 belong to this family." [GO:0007212, OneLook:www.onelook.com, PMID:17413183]
is_a: PW:0000394 ! dopamine signaling pathway
created_by: VPetri
creation_date: 2011-03-09T03:22:26Z

[Term]
id: PW:0000853
name: histamine signaling pathway
def: "Histamine signaling is important for the central and to some extent the peripheral nervous systems and is also involved in the immune responses. Histamine signaling in the brain involves receptors 1 and 3 that couple to Galphaq and Galphai, respectively." [OneLook:www.onelook.com]
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse
created_by: VPetri
creation_date: 2011-03-09T03:53:00Z

[Term]
id: PW:0000854
name: serotonin signaling pathway
def: "Serotonin signaling exerts many roles, from regulation of appetite, mood and sleep to involvement in learning and memory and in muscle contraction. Serotonin signals via several receptors known as 5-hydroxytryptamine or 5-HT receptors. With one exception, 5-HT receptors are G protein-coupled receptors engaging distinct G protein signaling to elicit distinct, both inhibitory and excitatory responses." [OneLook:www.onelook.com, PMID:18571247, PMID:18676031, PMID:20925600]
synonym: "KEGG:04726" RELATED []
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse
created_by: VPetri
creation_date: 2011-03-09T04:11:20Z

[Term]
id: PW:0000855
name: acetylcholine signaling pathway via muscarinic acetylcholine receptors engaging G alphaq protein family
def: "Acetylcholine signaling via receptor type M1, M3 and M5 primarily engages G alphaq protein family resulting in activation of phospholipase C and mobilization of intracellular calcium. The receptors are expressed in various areas of the brain such as the cerebral cortex and hippocampus. Receptor M3 is also found in smooth muscle; receptor M5 is found in the substantia nigra." [PMID:18082893]
is_a: PW:0000843 ! acetylcholine signaling pathway via muscarinic acetylcholine receptor
created_by: VPetri
creation_date: 2011-04-01T10:31:48Z

[Term]
id: PW:0000856
name: acetylcholine signaling pathway via muscarinic acetylcholine receptors engaging G alphai protein family
def: "Acetylcholine signaling via receptor type M2 and M4 primarily engages G alphai protein family resulting in inhibition of adenylate cyclases and reduction of intracellular cAMP. The receptors are expressed in various areas of the brain such as the cerebral cortex, hippocampus and the striatum. Receptor M2 is also expressed in smooth muscle, heart and lung." [PMID:18082893]
is_a: PW:0000843 ! acetylcholine signaling pathway via muscarinic acetylcholine receptor
created_by: VPetri
creation_date: 2011-04-01T11:01:32Z

[Term]
id: PW:0000857
name: phase I biotransformation pathway
def: "Phase I biotransformation pathway involves the conversion of exogenous substances to more polar metabolites. Members of the cytochrome P450 superfamily and to a lesser extent, flavin containing monooxygenases mediate the reactions." [PMID:19835560]
is_a: PW:0000124 ! cellular detoxification pathway
is_a: PW:0001229 ! xenobiotic metabolic pathway
created_by: VPetri
creation_date: 2011-04-04T04:25:01Z

[Term]
id: PW:0000858
name: phase II biotransformation pathway
def: "Phase II biotransformation pathway involves the conjugation of phase I products to various hydrophilic moieties that renders them more suitable for excretion. Various enzyme superfamilies are involved in carrying out the specific conjugation of metabolites." [PMID:19835560, PMID:20668491]
is_a: PW:0000124 ! cellular detoxification pathway
is_a: PW:0001229 ! xenobiotic metabolic pathway
created_by: VPetri
creation_date: 2011-04-04T04:37:36Z

[Term]
id: PW:0000859
name: glucuronidation conjugation pathway
def: "Glucuronidation of phase I products by members of the UDP-glucuronosyltranferase superfamily represents the major phase II conjugation pathway." [PMID:20668491]
is_a: PW:0000858 ! phase II biotransformation pathway
created_by: VPetri
creation_date: 2011-04-04T05:03:51Z

[Term]
id: PW:0000860
name: sulfonation conjugation pathway
def: "The sulfonation of phase I products by members of the sulfotransferase family represents a major route of phase II biotransformation, second to the glucuronidation pathway." [PMID:20668491]
is_a: PW:0000858 ! phase II biotransformation pathway
created_by: VPetri
creation_date: 2011-04-04T05:12:08Z

[Term]
id: PW:0000861
name: pyrimidine biosynthetic pathway
def: "Those enzymatic reactions involved in the synthesis of pyrimidine nucleotides. A major route for pyrimidine synthesis is the novo pathway. However, an alternate pathway, the salvage pathway, converts nucleosides generated by DNA or RNA breakdown back to nucleotide monophosphates which can then re-enter the biosynthetic pathway." [PMID:15096496, PMID:16098809]
is_a: PW:0000032 ! pyrimidine metabolic pathway
created_by: vpetri
creation_date: 2011-06-03T03:33:51Z

[Term]
id: PW:0000862
name: de novo pyrimidine biosynthetic pathway
def: "In the de novo biosynthetic pathway, pyrimidines are synthesized from simple precursors. Six reactions carried out by three genes in higher eukaryotes result in the formation of UMP, the precursor of all other pyrimidine nucleotides." [PMID:15096496, PMID:16098809]
is_a: PW:0000861 ! pyrimidine biosynthetic pathway
created_by: vpetri
creation_date: 2011-06-03T03:58:08Z

[Term]
id: PW:0000863
name: pyrimidine salvage pathway
def: "The salvage pathway of pyrimidine biosynthesis, mostly used in resting and differentiated cells, allows for the synthesis of pyrimidines from intermediates derived from DNA and RNA degradation pathways." [PMID:15096496, PMID:16098809]
is_a: PW:0000861 ! pyrimidine biosynthetic pathway
created_by: vpetri
creation_date: 2011-06-03T04:12:23Z

[Term]
id: PW:0000864
name: pyrimidine degradation pathway
def: "Those enzymatic reactions involved in the degradation of pyrimidines." [PMID:16098809]
is_a: PW:0000032 ! pyrimidine metabolic pathway
created_by: vpetri
creation_date: 2011-06-03T04:46:14Z

[Term]
id: PW:0000865
name: purine biosynthetic pathway
def: "Those enzymatic reactions involved in the synthesis of purine nucleotides. A major route for purine synthesis is the novo pathway. However, an alternate pathway, the salvage pathway, can also be used." [OneLook:www.onelook.com]
is_a: PW:0000031 ! purine metabolic pathway
created_by: VPetri
creation_date: 2011-06-06T04:49:00Z

[Term]
id: PW:0000866
name: purine degradation pathway
def: "Those enzymatic reactions involved in the degradation pathway of purines. Several enzymes are involved in the breakdown of adenine and guanine to uric acid. Primates, birds and other animal excrete uric acid. In other species uric acid is further metabolized to allantoin." [OneLook:www.onelook.com, RGD library:Lehringer Principles of Biochemistry]
is_a: PW:0000031 ! purine metabolic pathway
created_by: VPetri
creation_date: 2011-06-06T04:49:30Z

[Term]
id: PW:0000867
name: de novo purine biosynthetic pathway
def: "De novo purine biosynthesis requires ten enzymatic reactions to produce inosine monophosphate (IMP). Both adenine and guanine are then derived from IMP via several reactions. Purines are synthesized as nucleosides, i.e., as bases attached to ribose. Purines can also be created synthetically." [PMID:18712276]
is_a: PW:0000865 ! purine biosynthetic pathway
created_by: VPetri
creation_date: 2011-06-06T04:50:02Z

[Term]
id: PW:0000868
name: purine salvage pathway
is_a: PW:0000865 ! purine biosynthetic pathway
created_by: VPetri
creation_date: 2011-06-06T04:50:32Z

[Term]
id: PW:0000869
name: gefitinib drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of gefitinib. Gefitinib is the first selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:19657272, PMID:21196393]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2011-06-09T05:30:25Z

[Term]
id: PW:0000870
name: gefitinib pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of gefitinib. Gefitinib is the first selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA152325160&objCls=Pathway, PMID:15801543]
is_a: PW:0000869 ! gefitinib drug pathway
created_by: VPetri
creation_date: 2011-06-09T05:30:58Z

[Term]
id: PW:0000871
name: gefitinib pharmacodynamics pathway
def: "The pathway of gefitinib-target interactions and of the biochemical or physiological responses to drug. Gefitinib is the first selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can cause differences in the response of the organism to the drug." [PMID:21388312]
is_a: PW:0000869 ! gefitinib drug pathway
created_by: VPetri
creation_date: 2011-06-09T05:31:16Z

[Term]
id: PW:0000872
name: erlotinib drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of erlotinib. Erlotinib is the second (after gefitinib) selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:19657272, PMID:20072828]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2011-06-14T03:33:11Z

[Term]
id: PW:0000873
name: erlotinib pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of erlotinib. Erlotinib is the second (after gefitinib) selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA154426903&objCls=Pathway, PMID:19657272]
is_a: PW:0000872 ! erlotinib drug pathway
created_by: VPetri
creation_date: 2011-06-14T03:33:51Z

[Term]
id: PW:0000874
name: erlotinib pharmacodynamics pathway
def: "The pathway of erlotinib-target interaction and of the biochemical or physiological responses to drug. Erlotinib is the second (after gefitinib) selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can cause differences in the response of the organism to the drug." [PMID:20072828]
is_a: PW:0000872 ! erlotinib drug pathway
created_by: VPetri
creation_date: 2011-06-14T03:34:08Z

[Term]
id: PW:0000875
name: deoxyribonucleotide metabolic pathway
def: "Deoxyribonucleotide synthesis occurs via the de novo pathway mediated by ribonucleotide reductase or via the salvage pathway. The de novo pathway is responsible for the bulk of dNTP during the S phase of cell cycle whereas the salvage pathway mostly operates in the quiescent state of the cell. Several cytosolic and mitochondrial enzymes are responsible for the initial steps of the salvage pathway in the two compartments and for the reverse reactions that control the size of the dNTP pool." [PMID:15158709, PMID:16756507, PMID:17525869, PMID:20561600]
is_a: PW:0000012 ! nucleotide metabolic pathway
created_by: VPetri
creation_date: 2011-07-01T10:58:55Z

[Term]
id: PW:0000876
name: bacterial polysaccharide metabolic pathway
def: "Those metabolic reaction involved in the synthesis, utilization and/or degradation of polysaccharides that are components of bacterial cell wall. They may also act as virulence factors." [OneLook:www.onelook.com]
is_a: PW:0000146 ! glycan metabolic pathway
created_by: VPetri
creation_date: 2011-07-11T09:36:18Z

[Term]
id: PW:0000877
name: cytosine monophosphate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of cytosine monophosphate, the only nucleotide sugar in the monophosphate form." [OneLook:www.onelook.com]
is_a: PW:0000055 ! nucleotide sugar metabolic pathway
created_by: VPetri
creation_date: 2011-07-11T10:29:49Z

[Term]
id: PW:0000878
name: phosphatidylcholine biosynthetic pathway
def: "Phosphatidylcholine is the predominant phospholipid of eukaryotic membranes. Of the three known biosynthetic pathways, two are found in eukaryotes and one, the CDP-choline, is the best characterized." [PMID:15749057]
is_a: PW:0001307 ! phosphatidylcholine metabolic pathway
created_by: VPetri
creation_date: 2011-07-11T10:44:15Z

[Term]
id: PW:0000879
name: altered cortisol signaling pathway
def: "A cortisol signaling pathway that deviates from what its normal course should be. Mutations in the glucocorticoid receptor have been associated with rare, sporadic or familial, glucocorticoid resistance." [PMID:21448414]
is_a: PW:0000569 ! cortisol signaling pathway
is_a: PW:0000719 ! altered transcription factor mediated signaling pathway
is_a: PW:0000881 ! altered glucocorticoid signaling pathway
is_a: PW:0001314 ! altered transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2011-08-23T09:15:01Z

[Term]
id: PW:0000880
name: altered corticosteroid signaling pathway
is_a: PW:0000566 ! corticosteroid signaling pathway
created_by: VPetri
creation_date: 2011-08-23T09:19:49Z

[Term]
id: PW:0000881
name: altered glucocorticoid signaling pathway
is_a: PW:0000782 ! glucocorticoid signaling pathway
is_a: PW:0000880 ! altered corticosteroid signaling pathway
created_by: VPetri
creation_date: 2011-08-23T09:20:35Z

[Term]
id: PW:0000882
name: interleukin-1 family mediated signaling pathway
def: "The interleukin-1 family mediated signaling plays important roles in innate and adaptive immune responses. The best characterized member of the family is interleukin-1 followed by interleukin-18 and the more recently identified interleukin-33. Other family members are less well characterized." [PMID:20081871]
synonym: "Il-1 family mediated signaling pathway" RELATED []
is_a: PW:0000512 ! Interleukin mediated signaling pathway
created_by: VPetri
creation_date: 2011-08-29T11:08:06Z

[Term]
id: PW:0000883
name: interleukin-1 signaling pathway
def: "Interleukin-1 signaling, primarily via interleukin-1beta, plays important roles in innate and adaptive immune responses. Binding of the processed cytokine to its receptor, allows for the recruitment of several accessory and adaptor proteins leading to the activation of NF-kappaB and MAPK signaling cascades. A natural receptor antagonist and a decoy receptor act as regulators of interleukin 1alpha and beta." [PMID:20081871, PMID:20303867, PMID:21219179]
synonym: "Il-1 signaling pathway" EXACT []
synonym: "PID:200089" RELATED []
is_a: PW:0000882 ! interleukin-1 family mediated signaling pathway
is_a: PW:0000926 ! pro-inflammatory cytokine mediated pathway
created_by: VPetri
creation_date: 2011-08-29T11:15:28Z

[Term]
id: PW:0000884
name: interleukin-18 signaling pathway
def: "Interleukin-18 signaling plays important roles in innate and adaptive immunity. In the central nervous system (CNS), Il-18 and its receptors have been shown to play a role in neuroinflammatory and neurodegenerative processes as well as behavior and homeostasis. In addition, Il-18 may be a mediator of inflammation in rheumatoid arthritis." [PMID:20081871, PMID:20113500, PMID:21864160]
synonym: "Il-18 signaling pathway" RELATED []
is_a: PW:0000882 ! interleukin-1 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-08-29T11:16:18Z

[Term]
id: PW:0000885
name: interleukin-33 signaling pathway
def: "Interleukin-33 is the most recently discovered member of the interleukin-1 family. Like with the other members of the family, signaling by interleukin-33 plays important roles in inflammation and immunity and may be critical for the development of inflammatory and immune diseases." [PMID:20081871, PMID:21934731]
synonym: "Il-33 signaling pathway" RELATED []
is_a: PW:0000882 ! interleukin-1 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-08-29T11:16:46Z

[Term]
id: PW:0000886
name: interleukin-19 signaling pathway
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T09:28:03Z

[Term]
id: PW:0000887
name: interleukin-20 signaling pathway
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T09:37:36Z

[Term]
id: PW:0000888
name: interleukin-22 signaling pathway
def: "Interleukin-22 signaling triggers the Jak-Stat intracellular cascade resulting in the activation of various T helper (Th) cells." [PMID:11929132, PMID:20127093]
synonym: "Il-22 signaling pathway" RELATED []
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T09:38:18Z

[Term]
id: PW:0000889
name: interleukin-24 signaling pathway
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T09:39:50Z

[Term]
id: PW:0000890
name: interleukin-26 signaling pathway
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T09:40:28Z

[Term]
id: PW:0000891
name: interleukin-28A signaling pathway
synonym: "interferon lambda2 signaling pathway" RELATED []
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T10:26:15Z

[Term]
id: PW:0000892
name: interleukin-28B signaling pathway
synonym: "interferon lambda3 signaling pathway" RELATED []
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T10:29:31Z

[Term]
id: PW:0000893
name: interleukin-29 signaling pathway
synonym: "interferon lambda1 signaling pathway" RELATED []
is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T10:30:34Z

[Term]
id: PW:0000894
name: interferon mediated signaling pathway
def: "The interferons represent a subset of cytokines whose signaling is involved in various aspects of innate and adaptive immunity. Based on the type of receptors they employ, interferons have been classified into type I and II. A third type, the lambda interferons, are members of the interleukin 10 family." [PMID:17502369, PMID:20712454]
is_a: PW:0000828 ! cytokine mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T10:46:23Z

[Term]
id: PW:0000895
name: type I interferon signaling pathway
def: "Type I interferon, which includes all but one of the seven known human genes, binds to distinct receptors that activate the Jak-Stat signaling pathway." [PMID:17502369]
is_a: PW:0000894 ! interferon mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T10:58:32Z

[Term]
id: PW:0000896
name: type II interferon signaling pathway
def: "Type II interferon, of which there is only one in humans, binds to distinct receptors that activate Jak-Stat signaling pathway. It is known as the interferon gamma signaling." [PMID:17502369]
synonym: "interferon gamma signaling" RELATED []
synonym: "PID:200129" RELATED []
is_a: PW:0000894 ! interferon mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T11:07:25Z

[Term]
id: PW:0000897
name: interleukin-17 family mediated signaling pathway
def: "The interleukin-17 family mediated signaling plays important roles in inflammation and the development of autoimmunity as well as in the host defense against fungal and bacterial infections." [PMID:21349428]
synonym: "Il-17 family mediated signaling pathway" RELATED []
is_a: PW:0000512 ! Interleukin mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T11:23:23Z

[Term]
id: PW:0000898
name: interleukin-17E signaling pathway
def: "Interleukin-17E signaling, also known as interleukin-25, induces the production of Th2 cell cytokine leading to enhancement of Th2 cell responses." [PMID:21349428]
synonym: "Il-17E signaling pathway" RELATED []
synonym: "Il-25 signaling pathway" RELATED []
is_a: PW:0000897 ! interleukin-17 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T02:31:33Z

[Term]
id: PW:0000899
name: interleukin-17A signaling pathway
def: "Of the six family members of interleukin-17 family, interleukin-17A is the founding member and the better characterized system. While interleukin-17A binds the same receptor as interleukin-17F and can also heterodimerize with it, its signaling elicits distinct and broader responses." [PMID:21349428]
synonym: "Il-17A signaling pathway" RELATED []
is_a: PW:0000897 ! interleukin-17 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T02:31:40Z

[Term]
id: PW:0000900
name: interleukin-17F signaling pathway
def: "Interleukin-17F binds the same receptor as interleukin-17A and can also heterodimerize with it. However, its signaling while sharing features of interleukin-17A pathway also elicits distinct responses." [PMID:21349428]
is_a: PW:0000897 ! interleukin-17 family mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T02:41:48Z

[Term]
id: PW:0000901
name: altered interleukin mediated signaling pathway
def: "An interleukin mediated signaling pathway that deviates from what its normal course should be. Aberrant interleukin signaling pathway, alone or in combination with other pathways underlie various diseases." [InHouse:PW dictionary]
is_a: PW:0000512 ! Interleukin mediated signaling pathway
is_a: PW:0000617 ! altered cytokine mediated signaling pathway
created_by: VPetri
creation_date: 2011-12-06T03:18:18Z

[Term]
id: PW:0000902
name: interleukin-11 signaling pathway
is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway
created_by: vpetri
creation_date: 2012-01-23T04:17:23Z

[Term]
id: PW:0000903
name: leukemia inhibitory factor signaling pathway
synonym: "LIF signaling pathway" RELATED []
is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway
created_by: vpetri
creation_date: 2012-01-23T04:19:00Z

[Term]
id: PW:0000904
name: ciliary neurotrophic factor signaling pathway
synonym: "C" RELATED []
synonym: "CNTF signaling pathway" RELATED []
is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway
created_by: vpetri
creation_date: 2012-01-23T04:21:01Z

[Term]
id: PW:0000905
name: oncostatin M signaling pathway
synonym: "OSM signaling pathway" RELATED []
is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway
created_by: vpetri
creation_date: 2012-01-23T04:22:25Z

[Term]
id: PW:0000906
name: interleukin-2 family mediated signaling pathway
def: "Interleukin-2 family of cytokines, also known as gamma(c) family because of the shared gamma(c) receptor, plays crucial roles in the regulation of T cells." [PMID:19543225, PMID:21889323]
synonym: "Il-2 family mediated signaling pathway" RELATED []
is_a: PW:0000512 ! Interleukin mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T12:26:10Z

[Term]
id: PW:0000907
name: interleukin-2 signaling pathway
def: "Interleukin-2 is the prototypical member of the interleukin-2 family of cytokines. The signaling pathway initiated by Il-2 and the other family members activates the Jak-Stat intracellular cascade to regulate T cell, innate and adaptive immune responses." [PMID:19543225, PMID:21889323]
synonym: "Il-2 signaling pathway" EXACT []
synonym: "PID:200098" RELATED []
is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T12:33:40Z

[Term]
id: PW:0000908
name: interleukin-7 signaling pathway
is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T12:38:11Z

[Term]
id: PW:0000909
name: interleukin-9 signaling pathway
is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T12:39:11Z

[Term]
id: PW:0000910
name: interleukin-15 signaling pathway
is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T12:39:32Z

[Term]
id: PW:0000911
name: interleukin-21 signaling pathway
is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T12:39:52Z

[Term]
id: PW:0000912
name: interleukin-4 signaling pathway
def: "Interleukin-4 is a member of interleukin 2 family of cytokine whose signaling is important for the differentiation of naive T helper cells." [PMID:21889323]
synonym: "Il-4 signaling pathway" EXACT []
synonym: "PID:200022" RELATED []
is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T12:48:51Z

[Term]
id: PW:0000913
name: interleukin-12 family mediated signaling pathway
def: "Interleukin-12 family members of heterodimeric cytokines are produced by antigen presenting cells. The signaling they initiate triggers the Jak-Stat intracellular cascade and plays important roles in the regulation of T helper (Th) cell differentiation." [PMID:20885915]
synonym: "Il-12 family mediated signaling pathway" RELATED []
is_a: PW:0000512 ! Interleukin mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T03:39:11Z

[Term]
id: PW:0000914
name: interleukin-12 signaling pathway
def: "Interleukin-12 signaling activates the Jak-Stat intracellular cascade and promotes the differentiation and proliferation of Th1 cells and the production of interferon-gamma." [PMID:20885915, PMID:21553332]
synonym: "Il-12 signaling pathway" EXACT []
synonym: "PID:200045" RELATED []
is_a: PW:0000913 ! interleukin-12 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T03:43:43Z

[Term]
id: PW:0000915
name: interleukin-23 signaling pathway
synonym: "Il-23 signaling pathway" EXACT []
synonym: "PID:200154" RELATED []
is_a: PW:0000913 ! interleukin-12 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T03:49:27Z

[Term]
id: PW:0000916
name: interleukin-27 signaling pathway
synonym: "Il-27 signaling pathway" EXACT []
synonym: "PID:200028" RELATED []
is_a: PW:0000913 ! interleukin-12 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T03:49:45Z

[Term]
id: PW:0000917
name: interleukin-35 signaling pathway
is_a: PW:0000913 ! interleukin-12 family mediated signaling pathway
created_by: VPetri
creation_date: 2012-03-23T03:50:45Z

[Term]
id: PW:0000918
name: proton pump inhibitor drug pathway
def: "The pharmacokinetics and pharmacodynamics of proton pump inhibitor (PPI), a class of compounds that block the acid secretion from parietal cells in the stomach. A representative PPI compound is omeprazole. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/]
is_a: PW:0000921 ! alimentary tract and metabolism drug pathway
created_by: VPetri
creation_date: 2012-03-28T02:13:39Z

[Term]
id: PW:0000919
name: antineoplastic and immunomodulatory drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used as antineoplastic or as immunomodulatory agents. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2012-03-28T02:35:45Z

[Term]
id: PW:0000920
name: cardiovascular system drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of various cardiovascular conditions. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2012-03-28T02:45:12Z

[Term]
id: PW:0000921
name: alimentary tract and metabolism drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of alimentary tract and metabolism-related conditions. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2012-03-28T02:49:20Z

[Term]
id: PW:0000922
name: blood and blood forming organs drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of conditions associated with blood and blood forming organs. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2012-03-28T02:55:34Z

[Term]
id: PW:0000923
name: nervous system drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of conditions associated with the nervous system. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2012-03-28T02:58:10Z

[Term]
id: PW:0000924
name: respiratory system drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of conditions associated with the respiratory system. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2012-04-05T03:45:08Z

[Term]
id: PW:0000925
name: pattern recognition receptor mediated signaling pathway
def: "Pattern recognition receptors (PRR) respond to a diverse array of exogenous molecules and also several endogenous ones. PRR's 'sensing' of pathogen-associated molecular patterns (PAMP) or damage-associated (DAMP) prompts signaling cascades leading to the expression of pro-inflammatory genes." [MCW library:Cellular and molecular immunology\, by Abbas\, Abul K, PMID:20303867, PMID:20303872]
is_a: PW:0000024 ! inflammatory response pathway
is_a: PW:0000819 ! signaling pathway in the innate immune response
created_by: VPetri
creation_date: 2012-04-24T11:34:22Z

[Term]
id: PW:0000926
name: pro-inflammatory cytokine mediated pathway
def: "An early response of the innate immunity is the secretion of cytokines critical for the acute inflammatory response. The major pro-inflammatory cytokines are tumor necrosis factor alpha and the interleukins 1 and 6." [MCW library:cellular and molecular immunology\, by Abbas\, Abul K, PMID:20303867]
is_a: PW:0000024 ! inflammatory response pathway
created_by: VPetri
creation_date: 2012-04-24T11:43:45Z

[Term]
id: PW:0000927
name: anti-tumor necrosis factor drug pathway
def: "Tumor necrosis factor (TNF) inhibitors are used in the treatment of rheumatoid arthritis. The inhibitors are recombinant proteins that bind the soluble and membrane-associated TNF and inhibit the effects of this pro-inflammatory cytokine." [PMID:21039421]
synonym: "anti-TNF drug pathway" RELATED []
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-04-26T02:36:43Z

[Term]
id: PW:0000928
name: tocilizumab drug pathway
def: "Tocilizumab is a humanized anti-interleukin 6 (Il-6) receptor antibody used in the treatment of patients with rheumatoid arthritis, Castleman's disease or juvenile idiopathic arthritis. Tocilizumab binds to the soluble and membrane associated interleukin-6 receptor and competitively blocks binding of interleukin-6 to its receptor(s) and inhibits the effects of this potent cytokine." [PMID:21419125]
synonym: "Actemra drug pathway" RELATED []
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-04-26T03:00:42Z

[Term]
id: PW:0000929
name: anakinra drug pathway
def: "Anakinra is a recombinant, non-glycosylated version of the human interleukin-1 (Il-1) receptor antagonist used for the treatment of inflammation associated with rheumatoid arthritis. Like the natural antagonist, anakinra competitively inhibits binding of interleukin-1 to its receptor and the subsequent effects of this potent pro-inflammatory cytokine." [wikipedia:anakinra entry]
synonym: "kineret drug pathway" RELATED []
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-04-26T03:26:25Z

[Term]
id: PW:0000930
name: methotrexate drug pathway
def: "The pharmacokinetics and pharmacodynamics of methotrexate (MTX), a polyglutamatable antifolate used in the treatment of cancers and autoimmune diseases. The impact of MTX on cancer and rheumatoid arthritis is thought to arise through distinct mechanisms and pharmacodynamics pathways. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA2039]
synonym: "MTX drug pathway" EXACT []
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-04-27T01:27:25Z

[Term]
id: PW:0000931
name: methotrexate pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of methotrexate (MTX), a folate analogue used in the treatment of cancers and autoimmune diseases. Genetic variations can result in changes in the availability of the drug and It is believed that variability in MTX pharmacokinetics is linked to genetic variations in transporter proteins." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165816349]
synonym: "MTX pharmacokinetics pathway" EXACT []
is_a: PW:0000930 ! methotrexate drug pathway
created_by: VPetri
creation_date: 2012-04-27T01:46:47Z

[Term]
id: PW:0000932
name: methotrexate pharmacodynamics pathway
def: "The pathway of methotrexate-target interaction and of the biochemical or physiological responses to drug. The impact of MTX on cancer and rheumatoid arthritis is thought to arise through distinct mechanisms and pharmacodynamics pathways. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA2039]
synonym: "MTX pharmacodynamics pathway" EXACT []
is_a: PW:0000930 ! methotrexate drug pathway
created_by: VPetri
creation_date: 2012-04-27T02:16:39Z

[Term]
id: PW:0000933
name: tumor necrosis factor member 14 signaling pathway
def: "Tumor necrosis factor member 14, also known as Light, binds the lymphotoxin beta receptor and the tumor necrosis receptor member 14 known as Hvem of the tumor necrosis receptor superfamily to elicit important responses for the dendritic (DC) and T cells of the immune system." [PMID:11239407, PMID:12787557, PMID:2169337]
synonym: "Tnfsf14 (Light) signaling pathway" RELATED []
synonym: "Tnfsf14 signaling pathway" RELATED []
is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-01T10:26:22Z

[Term]
id: PW:0000934
name: tumor necrosis factor member 13 signaling pathway
def: "Tumor necrosis factor member 13 also known as April, binds the tumor necrosis factor receptor member 13B known as Taci and receptor member 17 known as Bcma of the tumor necrosis factor receptor superfamily to elicit important responses for the B cells of the immune system." [PMID:11239407, PMID:12787557, PMID:2169337]
synonym: "Tnfsf13 (April) signaling pathway" RELATED []
synonym: "Tnfsf13 signaling pathway" RELATED []
is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-01T11:00:20Z

[Term]
id: PW:0000935
name: tumor necrosis factor member 13b signaling pathway
def: "The tumor necrosis factor member 13b known as Baff binds to three receptor of the tumor necrosis factor receptor superfamily - the receptor member 13B known as Taci and member 17 known as Bcma to which member 13 of the ligand superfamily also binds, and additionally to member 13C of the receptor superfamily to elicit important responses for the B cells of the immune system." [PMID:11239407, PMID:12787557, PMID:2169337]
synonym: "Tnfsf13b (Baff) signaling pathway" RELATED []
synonym: "Tnfsf13b signaling pathway" RELATED []
is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-01T11:11:44Z

[Term]
id: PW:0000936
name: chemokine (C-C motif) ligand 1 signaling pathway
def: "Chemokine ligand 1 signaling engages the chemokine (C-C motif) receptor 8 (Ccr8) and together with other CC chemokines is classified as a member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl1 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T02:12:50Z

[Term]
id: PW:0000937
name: chemokine (C-C motif) ligand 2 signaling pathway
def: "Chemokine ligand 1 signaling engages the chemokine (C-C motif) receptor 2 (Ccr2) and together with other CC chemokines is classified as a member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl2 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T02:20:28Z

[Term]
id: PW:0000938
name: chemokine (C-C motif) ligand 3 signaling pathway
def: "Chemokine ligand 3 signaling pathway engages chemokine (C-C motif) receptors 2 and 5 (Ccr2 and Ccr5) and together with other chemokines is classified as a member of the pro-inflammatory subgroup." [PMID:15062643]
synonym: "Ccl3 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T02:30:19Z

[Term]
id: PW:0000939
name: chemokine (C-C motif) ligand 4 signaling pathway
def: "Chemokine ligand 4 signaling engages the chemokine (C-C motif) receptor 5 (Ccr5) and together with other chemokines is classified as a member of the pro-inflammatory subgroup." [PMID:15062643]
synonym: "Ccl4 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T02:34:32Z

[Term]
id: PW:0000940
name: chemokine (C-C motif) ligand 5 signaling pathway
def: "Chemokine ligand 5 signaling engages chemokine (C-C motif) receptors 1, 3 and 5 (Ccr1, Ccr3 and Ccr5) and together with other chemokines is classified as a member of the pro-inflammatory subgroup." [PMID:15062643]
synonym: "Ccl5 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T02:39:00Z

[Term]
id: PW:0000941
name: chemokine (C-C motif) ligand 6 signaling pathway
def: "Chemokine ligand 6 signaling is known to act in rodents and does not appear to have a human equivalent. Ccl6, together with other chemokines is classified as a member of the pro-inflammatory subgroup." [PMID:15062643]
synonym: "Ccl6 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T02:43:25Z

[Term]
id: PW:0000942
name: chemokine (C-C motif) ligand 7 signaling pathway
def: "Chemokine ligand 7 signaling engages chemokine (C-C) motif receptors 1, 2, and 3 (Ccr1, Ccr2, Ccr3) and together with other chemokines is classified as a member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl7 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T02:51:25Z

[Term]
id: PW:0000943
name: chemokine (C-C motif) ligand 8 signaling pathway
def: "Chemokine ligand 8 signaling engages chemokine (C-C motif) receptors 3 and 5 (Ccr3 and Ccr5) and together with other chemokines is classified as a member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl8 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T02:54:39Z

[Term]
id: PW:0000944
name: chemokine (C-C motif) ligand 11 signaling pathway
def: "Chemokine ligand 11 signaling engages the chemokine (C-C motif) receptor 3 (Ccr3) and together with other chemokines is classified as a member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl11 signaling pathway" EXACT []
synonym: "eotaxin signaling pathway" RELATED []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T03:09:44Z

[Term]
id: PW:0000945
name: chemokine (C-C motif) ligand 12 signaling pathway
def: "Chemokine ligand 12 signaling is known to act in rodents and does not appear to have a human equivalent. Ccl12, together with other chemokines is classified as a member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl12 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T03:16:03Z

[Term]
id: PW:0000946
name: chemokine (C-C motif) ligand 13 signaling pathway
def: "Chemokine ligand 13 signaling engages chemokine (C-C motif) receptors 2 and 3 (Ccr2 and Ccr3) and together with other chemokines is classified as a member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl13 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T03:17:54Z

[Term]
id: PW:0000947
name: chemokine (C-C motif) ligand 17 signaling pathway
def: "Chemokine ligand 17 signaling engages the chemokine (C-C motif) receptor 4 (Ccr4) and together with other chemokines is classified as a member of the developmental subgroup." [PMID:15062643]
synonym: "Ccl17 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T03:23:46Z

[Term]
id: PW:0000948
name: chemokine (C-C motif) ligand 22 signaling pathway
def: "Chemokine ligand 22 signaling engages the chemokine (C-C motif) receptor 4 (Ccr4) and together with other chemokines is classified as member of the developmental subgroup." [PMID:15062643]
synonym: "Ccl22 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T03:26:56Z

[Term]
id: PW:0000949
name: chemokine (C-C motif) ligand 25 signaling pathway
def: "Chemokine ligand 25 signaling engages the chemokine (C-C motif) receptor 9 (Ccr9) and together with other chemokines is classified as a member of the developmental subgroup." [PMID:15062643]
synonym: "Ccl25 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T03:31:08Z

[Term]
id: PW:0000950
name: chemokine (C-C motif) ligand 24 signaling pathway
def: "Chemokine ligand 24 signaling engages the chemokine (C-C motif) receptor 3 (Ccr3) and together with other chemokines is classified as member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl24 signaling pathway" EXACT []
synonym: "eotaxin-2 signaling pathway" RELATED []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T03:37:14Z

[Term]
id: PW:0000951
name: chemokine (C-C motif) ligand 26 signaling pathway
def: "Chemokine ligand 26 signaling engages the chemokine (C-C motif) receptor 3 (Ccr3) and together with other chemokines is classified as member of the allergenic subgroup." [PMID:15062643]
synonym: "Ccl26 signaling pathway" EXACT []
synonym: "eotaxin-3 signaling pathway" RELATED []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-01T03:39:19Z

[Term]
id: PW:0000952
name: chemokine (C-C motif) ligand 14 signaling pathway
def: "Chemokine ligand 14 signaling engages chemokine (C-C motif) receptors 1 and 5 (Ccr1 and Ccr5) and together with other chemokines is classified as a member of the HCC (hemofiltrate CC chemokine) subgroup." [PMID:15062643]
synonym: "Ccl14 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-02T03:16:19Z

[Term]
id: PW:0000953
name: chemokine (C-C motif) ligand 15 signaling pathway
def: "Chemokine ligand 15 signaling engages chemokine (C-C motif) receptors 1 and 3 (Ccr1 and Ccr3) and together with other chemokines is classified as a member of the HCC (hemofiltrate CC chemokine) subgroup." [PMID:15062643]
synonym: " Ccl15 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-02T03:32:48Z

[Term]
id: PW:0000954
name: chemokine (C-C motif) ligand 16 signaling pathway
def: "Chemokine ligand 16 signaling engages chemokine (C-C motif) receptors 1 and 2 (Ccr1 and Ccr2) and together with other chemokines is classified as a member of the HCC (hemofiltrate CC chemokine) subgroup." [PMID:15062643]
synonym: "Ccl16 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-02T03:34:53Z

[Term]
id: PW:0000955
name: chemokine (C-C motif) ligand 23 signaling pathway
def: "Chemokine ligand 23 signaling engages the chemokine (C-C motif) receptor 1 (Ccr1) and together with other chemokines is classified as a member of the HCC (hemofiltrate CC chemokine) subgroup." [PMID:15062643]
synonym: "Ccl23 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: vpetri
creation_date: 2012-05-02T03:37:10Z

[Term]
id: PW:0000956
name: chemokine (C-C motif) ligand 27 signaling pathway
def: "Chemokine ligand 27 signaling engages chemokine (C-C motif) receptor 10 (Ccr10) and does not appear to be a member of any of the chemokines subgroups." [PMID:15062643]
synonym: "Ccl27 signaling pathway" EXACT []
is_a: PW:0000831 ! CC chemokine mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-15T01:08:34Z

[Term]
id: PW:0000957
name: chemokine (C-X-C motif) ligand 1 signaling pathway
def: "Chemokine (C-X-C) ligand 1belongs to the growth-related oncogene (GRO) subgroup whose signaling engages receptor 2 and promotes chemotaxis of neutrophils." [PMID:18579287]
synonym: "Cxcl1 signaling pathway" EXACT []
synonym: "Gro alpha signaling pathway" RELATED []
is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-15T01:23:49Z

[Term]
id: PW:0000958
name: forkhead class A signaling pathway
def: "The signaling pathway mediated by the FoxA subgroup of forkhead family of transcription factors plays important roles in development and in modulating steroid hormone signaling. Three FoxA genes carry out overlapping yet distinct functions. FOXA1 appears to modulate steroid receptor activity in breast and prostate cancer." [PMID:19274050, PMID:20591647, PMID:21934649]
synonym: "FoxA signaling pathway" EXACT []
synonym: "PID:200087" RELATED []
synonym: "PID:200226" RELATED []
is_a: PW:0000647 ! forkhead signaling pathway
created_by: VPetri
creation_date: 2012-05-17T11:10:35Z

[Term]
id: PW:0000959
name: lipid signaling pathway
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2012-05-17T01:09:58Z

[Term]
id: PW:0000960
name: sphingosine 1-phosphate signaling pathway
def: "Sphingosine 1-phosphate (S1P), a sphingolipid metabolite, can signal intracellularly as a second messenger or extracellularly as a ligand for five G protein coupled receptors. S1P pathway plays important roles in processes such as cell migration, proliferation and survival. The five receptors engage similar G proteins but their expression varies." [PMID:18552276, PMID:22159476]
synonym: "PID:200046" RELATED []
synonym: "PID:200054" RELATED []
synonym: "PID:200076" RELATED []
synonym: "PID:200085" RELATED []
synonym: "PID:200123" RELATED []
synonym: "PID:200211" RELATED []
synonym: "S1P signaling pathway" RELATED []
is_a: PW:0000541 ! signaling pathway involving second messengers
is_a: PW:0000959 ! lipid signaling pathway
created_by: VPetri
creation_date: 2012-05-17T01:10:40Z

[Term]
id: PW:0000961
name: ceramide signaling pathway
def: "Ceramide signaling can act as a lipid second messenger or as a mediator of various cellular signaling pathways by promoting receptor clustering. The pathway plays important roles in apoptosis." [PMID:20607622]
synonym: "KEGG:05212" RELATED []
synonym: "PID:200119" RELATED []
is_a: PW:0000541 ! signaling pathway involving second messengers
is_a: PW:0000959 ! lipid signaling pathway
created_by: VPetri
creation_date: 2012-05-17T01:43:41Z

[Term]
id: PW:0000962
name: visual phototransduction pathway
def: "The signaling pathway initiated by light induced isomerization of 11-cis retinal and subsequent activation of its photoreceptors in rods and cones." [PMID:18514002, PMID:22074921]
synonym: "KEGG:04744" RELATED []
is_a: PW:0001008 ! photosignal transduction pathway
is_a: PW:0001116 ! vitamin A and metabolites signaling pathway
relationship: part_of PW:0001007 ! vitamin A homeostasis
created_by: VPetri
creation_date: 2012-05-17T05:16:34Z

[Term]
id: PW:0000963
name: phosphatidylinositol 3-kinase class I signaling pathway
def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivided into subclass A and B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PMID:16847462, PMID:17052169, PMID:17641274]
synonym: "PID:200116" RELATED []
is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway
created_by: VPetri
creation_date: 2012-05-18T10:40:25Z

[Term]
id: PW:0000964
name: altered phosphatidylinositol 3-kinase class I signaling pathway
is_a: PW:0000621 ! altered phosphatidylinositol 3-kinase signaling pathway
created_by: VPetri
creation_date: 2012-05-18T10:41:53Z

[Term]
id: PW:0000965
name: phosphatidylinositol 3-kinase class II signaling pathway
def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivided into subclass A and B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PMID:16847462, PMID:17052169, PMID:17641274]
is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway
created_by: VPetri
creation_date: 2012-05-18T10:50:58Z

[Term]
id: PW:0000966
name: phosphatidylinositol 3-kinase class III signaling pathway
def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivided into subclass A and B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PMID:16847462, PMID:17052169, PMID:17641274]
is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway
created_by: VPetri
creation_date: 2012-05-18T10:53:38Z

[Term]
id: PW:0000967
name: interleukin-3/interleukin-5/GM-CSF mediated signaling pathway
def: "Interleukin-3, interleukin 5 and granulocyte-macrophage colony-stimulating factors family of hemopoietic cytokine mediate overlapping and distinct signals. Collectively they regulate the production and activation of hemopoietic cells." [PMID:19436055]
synonym: "hemopoietic cytokine family mediated signaling pathway" RELATED []
synonym: "Il-3/Il-5/GM-CSF family mediated signaling pathway" EXACT []
is_a: PW:0000512 ! Interleukin mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T11:30:25Z

[Term]
id: PW:0000968
name: interleukin-3 signaling pathway
def: "Interleukin-3 signaling plays important roles in the function of hematopoietic cells." [PMID:11312115]
synonym: "Il-3 signaling pathway" EXACT []
synonym: "PID:200145" RELATED []
is_a: PW:0000967 ! interleukin-3/interleukin-5/GM-CSF mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T11:43:49Z

[Term]
id: PW:0000969
name: interleukin-5 signaling pathway
def: "Interleukin-5 signaling plays important roles in the function of hematopoietic cells." [PMID:11312115]
synonym: "Il-5 signaling pathway" EXACT []
synonym: "PID:200107" RELATED []
is_a: PW:0000967 ! interleukin-3/interleukin-5/GM-CSF mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T11:44:14Z

[Term]
id: PW:0000970
name: granulocyte-macrophage colony-stimulating factor signaling pathway
def: "GM-CSF signaling, like the other hemopoietic cytokines, is involved in the production and activation of hemopoietic cells. The GM-CSF pathway acts on monocytes, macrophages and granulocytes and is also involved in the regulation of T and dendritic cells functions." [PMID:19436055]
synonym: "GM-CSF signaling pathway" EXACT []
synonym: "PID:200019" RELATED []
is_a: PW:0000967 ! interleukin-3/interleukin-5/GM-CSF mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T11:44:40Z

[Term]
id: PW:0000971
name: CXC chemokine ELR(+) subgroup mediated signaling pathway
def: "The CXC chemokine ELR(+) subgroup mediated signaling primarily engages receptor 2 to promote angiogenic effects." [PMID:18579287]
is_a: PW:0000830 ! CXC chemokine mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T02:49:53Z

[Term]
id: PW:0000972
name: CXC chemokine ELR(-) subgroup mediated signaling pathway
def: "CXC chemokine (ELR-) subgroup mediated signaling primarily engages receptor 3 to promote angiostatic effects." [PMID:18579287]
is_a: PW:0000830 ! CXC chemokine mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T02:49:59Z

[Term]
id: PW:0000973
name: chemokine (C-X-C motif) ligand 2 signaling pathway
def: "Chemokine (C-X-C) ligand 2 belongs to the growth-related oncogene (GRO) subgroup whose signaling engages receptor 2 to promote chemotaxis of neutrophils." [PMID:18579287]
synonym: "Cxcl2 signaling pathway" EXACT []
synonym: "Gro beta signaling pathway" RELATED []
is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T03:26:21Z

[Term]
id: PW:0000974
name: chemokine (C-X-C motif) ligand 3 signaling pathway
def: "Chemokine (C-X-C) ligand 3 belongs to the growth-related oncogene (GRO) subgroup whose signaling engages receptor 2 to promote chemotaxis of neutrophils." [PMID:18579287]
synonym: "Cxcl3 signaling pathway" EXACT []
synonym: "Gro gamma signaling pathway" RELATED []
is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T03:29:34Z

[Term]
id: PW:0000975
name: chemokine (C-X-C motif) ligand 5 signaling pathway
def: "Chemokine (C-X-C) ligand 5 signaling engages receptor 2 to exert potent chemotactic functions in neutrophil activation." [PMID:18579287]
synonym: "Cxcl5 signaling pathway" EXACT []
synonym: "Ena-78 signaling pathway" RELATED []
is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T03:37:57Z

[Term]
id: PW:0000976
name: chemokine (C-X-C motif) ligand 6 signaling pathway
def: "Chemokine (C-X-C0) ligand 6 engages receptors 1 and 2 to promote chemoattraction of neutrophils and angiogenic effects, respectively." [PMID:18579287]
synonym: "Cxcl6 signaling pathway" EXACT []
is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T03:42:45Z

[Term]
id: PW:0000977
name: chemokine (C-X-C motif) ligand 7 signaling pathway
is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T03:48:29Z

[Term]
id: PW:0000978
name: chemokine (C-X-C motif) ligand 8 signaling pathway
def: "Chemokine (C-X-C) ligand 8, also known as interleukin-8 (Il-8), although a chemokine, engages receptor 1 and 2 to promote angiogenic effects." [PMID:18579287]
synonym: "Cxcl8 signaling pathway" EXACT []
synonym: "Il-8 signaling pathway" RELATED []
synonym: "PID:200136" RELATED []
is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T03:49:12Z

[Term]
id: PW:0000979
name: chemokine (C-X-C motif) ligand 4 signaling pathway
def: "Chemokine (C-X-C) ligand 4 signaling engages receptor 3 to promote angiostatic effects." [PMID:18579287]
synonym: "Cxcl4 signaling pathway" EXACT []
is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T03:55:01Z

[Term]
id: PW:0000980
name: chemokine (C-X-C motif) ligand 9 signaling pathway
def: "Chemokine (C-X-C) ligand 9 engages receptor 3 to promote angiostatic effects." [PMID:18579287]
synonym: "Cxcl9 signaling pathway" EXACT []
synonym: "Mig signaling pathway" RELATED []
is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T03:57:41Z

[Term]
id: PW:0000981
name: chemokine (C-X-C motif) ligand 10 signaling pathway
def: "Chemokine (C-X-C) ligand 10 signaling engages receptor 3 to promote angiostatic effects." [PMID:18579287]
synonym: "Cxcl10 signaling pathway" EXACT []
is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T04:00:20Z

[Term]
id: PW:0000982
name: chemokine (C-X-C motif) ligand 11 signaling pathway
def: "Chemokine (C-X-C) ligand 11 signaling engages receptor 3 to promote angiostatic effects." [PMID:18579287]
synonym: "Cxcl11 signaling pathway" EXACT []
is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T04:10:07Z

[Term]
id: PW:0000983
name: chemokine (C-X-C motif) ligand 12 signaling pathway
is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T05:01:33Z

[Term]
id: PW:0000984
name: chemokine (C-X-C motif) ligand 13 signaling pathway
is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T05:02:28Z

[Term]
id: PW:0000985
name: chemokine (C-X-C motif) ligand 14 signaling pathway
is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T05:03:13Z

[Term]
id: PW:0000986
name: chemokine (C-X-C motif) ligand 16 signaling pathway
is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-22T05:04:00Z

[Term]
id: PW:0000987
name: erythropoietin signaling pathway
def: "Erythropoietin (EPO) signaling is crucial for the production of blood cell or erythropoiesis and also plays important roles in wound healing and responses to neural injury. EPO is a glycoprotein hormone and also a cytokine whose receptor belongs to type I cytokine receptor. The pathway engages the Jak-Stat intracellular cascade." [OneLook:www.onelook.com, PMID:21307776]
synonym: "EPO signaling pathway" EXACT []
synonym: "PID:200183" RELATED []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
is_a: PW:0000828 ! cytokine mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-24T02:57:05Z

[Term]
id: PW:0000988
name: classical cadherin signaling pathway
def: "Classical cadherins, such as E- or N-cadherin are single-span transmembrane proteins with five extracellular cadherin repeats and a conserved cytoplasmic tail. Their interaction with many cytoskeletal and signaling molecules underlies the calcium-dependent cell-cell adhesion and signaling. While E- and N-cadherin share some of the interacting partners, they have different localization and impact on distinct cellular events." [PMID:11171368, PMID:21444749]
is_a: PW:0000333 ! cadherin mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-25T10:07:46Z

[Term]
id: PW:0000989
name: desmosomal cadherin signaling pathway
def: "Desmosomal cadherins, which can be further subdivided into two subgroups, possess the five cadherin repeats but have distinct cytoplasmic tails." [PMID:11171368]
is_a: PW:0000333 ! cadherin mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-25T10:37:23Z

[Term]
id: PW:0000990
name: protocadherin signaling pathway
def: "Protocadherin represent a very large family which can be further subdivided into two groups. The protocadherin are predominantly expressed in the nervous system. They have up to seven cadherin repeats but distinct and even divergent cytoplasmic regions." [PMID:11171368, PMID:17936607]
is_a: PW:0000333 ! cadherin mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-25T10:37:53Z

[Term]
id: PW:0000991
name: atypical cadherin signaling pathway
def: "The atypical, or unconventional group includes the seven transmembrane (7TM), GPCR-like cadherins with up to nine cadherin repeats along with EGF-like and laminin motifs, the large FAT and the t-Cadherin proteins." [PMID:11171368]
is_a: PW:0000333 ! cadherin mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-25T10:38:11Z

[Term]
id: PW:0000992
name: E-cadherin signaling pathway
def: "E-cadherin or the epithelial cadherin encoded by the Cdh1 gene, is a member of the classical cadherin family and among the best studied cadherin pathway. Deregulation of the pathway has been associated with several forms of cancer." [PMID:11171368, PMID:21444749]
synonym: "Cdh1 signaling pathway" RELATED []
synonym: "PID:200124" RELATED []
synonym: "PID:200147" RELATED []
synonym: "PID:200182" RELATED []
is_a: PW:0000988 ! classical cadherin signaling pathway
created_by: VPetri
creation_date: 2012-05-25T10:51:52Z

[Term]
id: PW:0000993
name: N-cadherin signaling pathway
def: "N-cadherin, or neuronal cadherin, is predominantly expressed in the brain. The pathway plays important roles in learning and memory." [PMID:11171368, PMID:21444749]
synonym: "Cdh2 signaling pathway" RELATED []
synonym: "PID:200209" RELATED []
is_a: PW:0000988 ! classical cadherin signaling pathway
created_by: VPetri
creation_date: 2012-05-25T10:52:18Z

[Term]
id: PW:0000994
name: altered classical cadherin signaling pathway
is_a: PW:0000338 ! altered cadherins mediated signaling pathway
is_a: PW:0000988 ! classical cadherin signaling pathway
created_by: VPetri
creation_date: 2012-05-25T11:18:01Z

[Term]
id: PW:0000995
name: altered E-cadherin signaling pathway
is_a: PW:0000992 ! E-cadherin signaling pathway
is_a: PW:0000994 ! altered classical cadherin signaling pathway
created_by: VPetri
creation_date: 2012-05-25T11:18:51Z

[Term]
id: PW:0000996
name: anti-infective drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used as anti-infective agents. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
synonym: "anti-infective drug pathway" EXACT []
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2012-05-25T11:37:29Z

[Term]
id: PW:0000997
name: nucleoside and nucleotide mediated signaling pathway
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2012-05-25T11:48:24Z

[Term]
id: PW:0000998
name: adenosine signaling pathway
def: "Adenosine signaling is involved in the regulation of several physiological processes. It uses four receptors of the GPCR family that activate the Gaphas and Galphai types of G proteins to increase or decrease the levels of cAMP. The adenosine receptors are a class of purinergic or purinoreceptors." [PMID:21185259, PMID:21622100]
is_a: PW:0000997 ! nucleoside and nucleotide mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-25T11:53:37Z

[Term]
id: PW:0000999
name: adenosine triphosphate signaling pathway
def: "Adenosine triphosphate (ATP) extracellular signaling activates the P2X ligand-gated ion channels that are permeable to sodium, potassium and calcium ions. There are several P2X subtypes that are involved in a range of physiological processes. ATP along with other nucleotide also engages a class of metabotropic purinergic receptors known as P2Y that couple to either the Galphaq or to G alphai subunit of heterotrimeric G proteins. ATP is the sole ligand of P2Y 11 receptor." [PMID:21586365, PMID:22535247]
synonym: "ATP signaling pathway" EXACT []
is_a: PW:0000997 ! nucleoside and nucleotide mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-25T12:03:02Z

[Term]
id: PW:0001000
name: nucleotide signaling via the purinergic P2Y receptors.
def: "The P2Y receptors are a class of purinergic or purinoreceptors, Gprotein-coupled receptors that respond to ADP, ATP, UDP, UTP and UDP-glucose to activate either the Galphaq or the Galphai mediated signal transduction pathways." [PMID:16968944, PMID:20594935]
is_a: PW:0000997 ! nucleoside and nucleotide mediated signaling pathway
created_by: VPetri
creation_date: 2012-05-25T12:11:33Z

[Term]
id: PW:0001001
name: adenosine triphosphate signaling via the P2X ligand-gated ion channel
synonym: "ATP signaling via the P2X ligand-gated ion channel" EXACT []
is_a: PW:0000999 ! adenosine triphosphate signaling pathway
created_by: VPetri
creation_date: 2012-05-30T02:32:59Z

[Term]
id: PW:0001002
name: copper homeostasis pathway
is_a: PW:0000589 ! metal homeostasis pathway
created_by: VPetri
creation_date: 2012-05-31T04:20:42Z

[Term]
id: PW:0001003
name: retinoid metabolic pathway
def: "Those metabolic reactions involving the fat-soluble vitamin A and its metabolites. Vitamin A, retinol and vitamin A activities of metabolites such as retinal and retinoic acids are essential for visual transduction as well as for neuro and immune system functions and epithelial differentiation. Plants and microorganisms can synthesize vitamin A de novo while higher organisms derive it from diet as precursors carotenoids or retinyl esters." [PMID:21554983]
synonym: "vitamin A metabolic pathway" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients
relationship: part_of PW:0001007 ! vitamin A homeostasis
created_by: VPetri
creation_date: 2012-06-04T10:52:32Z

[Term]
id: PW:0001004
name: retinoic acid metabolic pathway
def: "The reactions involved in deriving retinoic acid (RA) from retinal and its further processing to more polar derivatives. Retinoic acid engages several retinoic acid receptors; its actions are important for the neuro and immune system functions and energy balance. Deregulation of proper RA activity has been associated with obesity and cancer." [PMID:21621639]
synonym: "RA metabolic pathway" EXACT []
is_a: PW:0001003 ! retinoid metabolic pathway
created_by: VPetri
creation_date: 2012-06-04T11:05:02Z

[Term]
id: PW:0001005
name: retinoid cycle metabolic pathway
def: "The series of reactions involved in the regeneration of the visual chromophore 11-cis retinal from the all-trans retinal released from the light -activated rhodopsin." [PMID:21447403]
synonym: "visual cycle metabolic pathway" EXACT []
is_a: PW:0001003 ! retinoid metabolic pathway
created_by: VPetri
creation_date: 2012-06-04T11:19:05Z

[Term]
id: PW:0001006
name: vitamin homeostasis
is_a: PW:0000355 ! homeostasis pathway
created_by: VPetri
creation_date: 2012-06-04T01:28:58Z

[Term]
id: PW:0001007
name: vitamin A homeostasis
def: "The pathways involved in the balanced maintenance of vitamin A and vitamin A metabolites uptake and transport, utilization and storage, as demanded by the needs of cells, tissues and organs. 11-cis retinal is the visual chromophore while retinoic acid signaling through its nuclear receptors transcription factors exerts the rest and manifold functions of vitamin A." [PMID:21554983, PMID:21586336, PMID:21621639]
synonym: "vitamin A homeostasis" EXACT []
is_a: PW:0001006 ! vitamin homeostasis
created_by: VPetri
creation_date: 2012-06-04T01:30:04Z

[Term]
id: PW:0001008
name: photosignal transduction pathway
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2012-06-05T10:44:24Z

[Term]
id: PW:0001009
name: ascorbic acid metabolic pathway
def: "Those metabolic reactions involving ascorbic acid, known as vitamin C, a water-soluble vitamin. Vitamin C is an essential antioxidant that is derived from glucose. Unlike many animals, humans do not have the ability to produce it. Vitamin C acts as an antioxidant." [OneLook:http\://www.onelook.com]
synonym: "vitamin C metabolic pathway" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients
created_by: VPetri
creation_date: 2012-06-05T11:40:08Z

[Term]
id: PW:0001010
name: niacin metabolic pathway
def: "Those metabolic reactions involving niacin, also known as vitamin B3 or vitamin PP - a water-soluble vitamin. Niacin represents an essential nutrient and is also a precursor of NAD through a salvage pathway. Niacin is among the few vitamins humans can synthesize." [OneLoook:http\://www.onelook.com]
synonym: "KEGG:00760" RELATED []
synonym: "vitamin B3 metabolic pathway" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients
created_by: VPetri
creation_date: 2012-06-05T11:44:25Z

[Term]
id: PW:0001011
name: vitamin D metabolic pathway
def: "Those metabolic reactions involving vitamin D - a fat-soluble vitamin. Vitamin D represents a group of fat-soluble compounds that can be synthesized from cholesterol and exposure to sunlight. In view of the latter source, it is not considered a true vitamin. One of its metabolites, calcitriol acts in a hormone-like manner as a signaling molecule." [OneLook:http\://www.onelook.com]
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients
created_by: VPetri
creation_date: 2012-06-05T12:01:10Z

[Term]
id: PW:0001012
name: vitamin and vitamin metabolites signaling pathway
def: "Vitamin and metabolites of vitamin in addition to representing important nutrients and aid in cellular metabolism can also, in a hormone-like manner, acts as signaling molecules." [PMID:22020178, PMID:22318625, PMID:22614789]
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2012-06-05T12:07:26Z

[Term]
id: PW:0001013
name: vitamin D signaling pathway
def: "The active vitamin D metabolite plays important roles in cell growth and differentiation and in immunity. Its receptor is a transcription factor nuclear receptor." [PMID:22213316]
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001012 ! vitamin and vitamin metabolites signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2012-06-05T12:13:52Z

[Term]
id: PW:0001014
name: retinoic acid signaling pathway
def: "Retinoic acid, a vitamin A-derived metabolite plays important roles in development and cell differentiation. all-trans retinoic acid (RA) binds to nuclear RA (RARs) and X (RXRs) receptor subtypes that once activated act as transcription factors." [PMID:22020178, PMID:22318625]
synonym: "RA signaling pathway" EXACT []
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001116 ! vitamin A and metabolites signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
relationship: part_of PW:0001007 ! vitamin A homeostasis
created_by: VPetri
creation_date: 2012-06-05T12:22:48Z

[Term]
id: PW:0001015
name: vitamin E metabolic pathway
def: "Those metabolic reactions involving vitamin E - a fat-soluble vitamin which represents a class of chemical compounds known as tocopherols. The alpha- and gamma-tocopherols appear to be the main dietary forms. Vitamin E is best known for its antioxidant properties." [PMID:15256801]
synonym: "tocopherol metabolic pathway" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients
created_by: VPetri
creation_date: 2012-06-11T01:34:39Z

[Term]
id: PW:0001016
name: vitamin K metabolic pathway
def: "Those metabolic reactions involving vitamin K - a fat-soluble vitamin which represents a group of related compounds. K1 and K2 are the main naturally-occurring forms. Vitamin K is an essential cofactor for many vitamin K-dependent proteins such as several coagulation factors or the anticoagulant proteins C and S." [PMID:21968919, PMID:22407747]
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients
created_by: VPetri
creation_date: 2012-06-11T01:46:25Z

[Term]
id: PW:0001017
name: renal cell cancer pathway
def: "Renal cell cancer, although representing a small percentage of human neoplasms, has one of the highest rate of mortality amongst genitourinary cancers. Several mutated genes and associated altered pathways have been implicated in the condition but many more remain to be elucidated." [PMID:22112490]
synonym: "KEGG:05211" RELATED []
is_a: PW:0000606 ! urogenital cancer pathway
created_by: VPetri
creation_date: 2012-07-03T01:03:23Z

[Term]
id: PW:0001018
name: immune disease pathway
is_a: PW:0000013 ! disease pathway
created_by: VPetri
creation_date: 2012-07-03T01:17:41Z

[Term]
id: PW:0001019
name: rheumatoid arthritis pathway
def: "The rheumatoid arthritis is an autoimmune condition characterized by persistent inflammation. Several pro-inflammatory cytokine and chemokines are overactivated." [PMID:22357455]
synonym: "KEGG:05323" RELATED []
is_a: PW:0001440 ! arthritis disease pathway
created_by: VPetri
creation_date: 2012-07-03T01:18:10Z

[Term]
id: PW:0001020
name: basal cell carcinoma pathway
def: "Basal cell carcinoma is the most common form of skin cancer that is mostly sporadic. Hedgehog signaling pathway via sonic hedgehog appears to be constitutively active. Mutations in Tp53 are also frequent." [OneLook:www.onelook.com]
synonym: "KEGG:05217" RELATED []
is_a: PW:0000633 ! skin cancer pathway
created_by: VPetri
creation_date: 2012-07-10T12:40:11Z

[Term]
id: PW:0001021
name: melanoma pathway
def: "Melanoma is a form of skin cancer which, despite being less common than other form of skin malignancies, it can be dangerous if not detected earlier and it accounts for the highest percentage if skin cancer related deaths. Oncogenic Nras and other mutations in downstream pathways appear to be associated with it." [OneLook:www.onelook.com]
synonym: "KEGG:05218" RELATED []
is_a: PW:0000633 ! skin cancer pathway
created_by: VPetri
creation_date: 2012-07-10T12:47:47Z

[Term]
id: PW:0001022
name: asthma disease pathway
def: "Asthma, a complex condition with many phenotypic manifestations, is primarily characterized by inflammation of the airways. Environmental and genetic factors contribute to it through complex and incompletely understood interactions." [OneLook:http\://www.onelook.com]
synonym: "KEGG:05310" RELATED []
is_a: PW:0001018 ! immune disease pathway
created_by: VPetri
creation_date: 2012-07-10T01:39:57Z

[Term]
id: PW:0001023
name: systemic lupus erythematosus pathway
def: "Systemic lupus erythematosus (SLE) is an autoimmune condition that can affect many parts of the body and which, although treatable, does not have a cure. Activation of complement and deregulations of immune regulatory and signaling pathways contribute in ways that are incompletely understood." [OneLook:http\://www.onelook.com]
synonym: "KEGG:05322" RELATED []
synonym: "SLE pathway" EXACT []
is_a: PW:0001018 ! immune disease pathway
created_by: VPetri
creation_date: 2012-07-10T01:48:28Z

[Term]
id: PW:0001024
name: autoimmune thyroid disease pathway
def: "Autoimmune thyroid disease (AITD) groups several conditions generally relatively mild but that can progress to serious symptoms." [localhealth:http\://www.localhealth.com]
synonym: "AITD pathway" EXACT []
synonym: "KEGG:05320" RELATED []
is_a: PW:0001018 ! immune disease pathway
created_by: VPetri
creation_date: 2012-07-10T01:56:40Z

[Term]
id: PW:0001025
name: allograft rejection pathway
def: "Allograft, or transplant rejection, results from the recipient's autoimmune response to the nonself antigens." [OneLook:www.onelook.com]
synonym: "KEGG:05330" RELATED []
is_a: PW:0001018 ! immune disease pathway
created_by: VPetri
creation_date: 2012-07-11T10:38:17Z

[Term]
id: PW:0001026
name: graft-versus-host disease pathway
def: "Graft-versus-host disease (GVHD) is a complication following transplantation of cells, tissues or organs from a genetically non-identical donor in which the donor T cells attack the host cells. Several pro-inflammatory pathways are activated as a result of damage in the host tissue induced by the procedure. GVHD is commonly associated with stem cell or bone marrow transplant." [OneLook:http\://www.onelook.com]
synonym: "GVHD pathway" EXACT []
synonym: "KEGG:05332" RELATED []
is_a: PW:0001018 ! immune disease pathway
created_by: VPetri
creation_date: 2012-07-11T10:43:26Z

[Term]
id: PW:0001027
name: primary immunodeficiency disease pathway
def: "Primary immunodeficiency groups disorders that result from the immune system malfunctioning that affect both cell-mediated and humoral immunity pathways." [OneLook:http\://www.onelook.com]
synonym: "KEGG:05340" RELATED []
is_a: PW:0001018 ! immune disease pathway
created_by: VPetri
creation_date: 2012-07-11T10:56:46Z

[Term]
id: PW:0001028
name: infectious disease pathway
def: "Infectious diseases are caused by pathogens that have gained access to the host organism and have managed to avoid the host defense mechanisms while taking over some of the host pathways." [OneLook:http\://www.onelook.com]
synonym: "communicable disease pathway" RELATED []
synonym: "transmissible disease pathway" RELATED []
is_a: PW:0000013 ! disease pathway
created_by: VPetri
creation_date: 2012-07-11T11:07:42Z

[Term]
id: PW:0001029
name: substance dependence disease pathway
is_a: PW:0000013 ! disease pathway
created_by: VPetri
creation_date: 2012-07-11T11:08:32Z

[Term]
id: PW:0001030
name: cocaine addiction pathway
def: "Prolonged use of cocaine results in cardiovascular and brain damage. Cocaine is thought to bind to the dopamine reuptake transporter thus blocking the reuptake of dopamine into nerve terminals. The resulting higher concentration of dopamine in synapses leads to overactivation of dopamine receptors such as D1 and of signaling pathways downstream of it overall believed to be critical in mediating the behavioral responses to cocaine." [KEGG:map05030, OneLook:http\://www.onelook.com]
synonym: "KEGG:05030" RELATED []
is_a: PW:0001029 ! substance dependence disease pathway
created_by: VPetri
creation_date: 2012-07-11T11:18:43Z

[Term]
id: PW:0001031
name: amphetamine addiction pathway
def: "Amphetamine is believed to promote an elevation in extracellular dopamine. Higher and high levels of the drug lead to overactivation of transcription factors and cofactors." [KEGG:map\:05031, OneLook:http\://www.onelook.com]
synonym: "KEGG:05031" RELATED []
is_a: PW:0001029 ! substance dependence disease pathway
created_by: VPetri
creation_date: 2012-07-11T11:31:37Z

[Term]
id: PW:0001032
name: morphine addiction pathway
def: "Morphine, an effective pain killer drug, can also be extremely addictive. Activation of dopamine neurons and reduction of inhibitory synaptic transmission might be associated with the effects or morphine. Changes in neuronal responses and communication may underlie the addictive behavior." [KEGG:map05032, OneLook:http\://www.onelook.com]
synonym: "KEGG:05032" RELATED []
is_a: PW:0001029 ! substance dependence disease pathway
created_by: VPetri
creation_date: 2012-07-11T11:41:36Z

[Term]
id: PW:0001033
name: nicotine addiction pathway
def: "Nicotine, like the other addictive substances, impacts on the dopaminergic and mesolimbic reward circuitries. Nicotine is also a ligand for the nicotinic acetylcholine receptors which are ligand-gated ion channels." [KEGG:map05033, OneLook:http\://www.onelook.com]
synonym: "KEGG:05033" RELATED []
is_a: PW:0001029 ! substance dependence disease pathway
created_by: VPetri
creation_date: 2012-07-11T11:46:55Z

[Term]
id: PW:0001034
name: alcoholism pathway
def: "The mechanisms of alcohol dependence, or alcoholism, are not well understood. Like in the case of other substances of abuse, alcohol may lead to stimulation of dopamine release and overactivation of dopamine-related circuitries." [KEGG:map05034, OneLook:http\://www.onelook.com]
synonym: "alcohol dependence pathway" EXACT []
synonym: "KEGG:05034" RELATED []
is_a: PW:0001029 ! substance dependence disease pathway
created_by: VPetri
creation_date: 2012-07-11T11:57:05Z

[Term]
id: PW:0001035
name: arrhythmogenic right ventricular cardiomyopathy pathway
def: "Arrhythmogenic right ventricular cardiomyopathy (ARVC) represents an inherited heart muscle condition leading to arrhythmia and heart failure that could results in death. Mutations in several genes and disruption of associated pathways have been implicated in the condition." [KEGG:map05412, OneLook:http\://www.onelook.com]
synonym: "ARVC pathway" EXACT []
synonym: "KEGG:05412" RELATED []
is_a: PW:0000022 ! cardiomyopathy pathway
created_by: VPetri
creation_date: 2012-07-11T12:12:10Z

[Term]
id: PW:0001036
name: dilated cardiomyopathy pathway
def: "Dilated cardiomyopathy (DCM) is a condition in which the heart is weakened and enlarged resulting in inefficient blood pumping. Although mostly occurring in adults, it can also affect children." [KEGG:map05414, OneLook:http\://www.onelook.com]
synonym: "DCM pathway" EXACT []
synonym: "KEGG:05414" RELATED []
is_a: PW:0000022 ! cardiomyopathy pathway
created_by: VPetri
creation_date: 2012-07-11T12:20:46Z

[Term]
id: PW:0001037
name: myocarditis pathway
def: "Myocarditis, a condition associated with inflammation of the heart muscle that can have both infections and non-infectious etiologies with the former being the primary cause. Viral proteins, once inside the host cells interfere with the function of host gene and they can either avoid or appropriate host pathways." [KEGG:map05416, OneLook:http\://www.onelook.com]
synonym: "KEGG:05416" RELATED []
is_a: PW:0000022 ! cardiomyopathy pathway
created_by: VPetri
creation_date: 2012-07-11T12:29:11Z

[Term]
id: PW:0001038
name: maturity onset diabetes of the young pathway
def: "Maturity onset diabetes of the young (MODY) represents any of a number of hereditary, monogenic forms of diabetes caused by mutations in several genes." [KEGG:map04950, OneLoook:http\://www.onelook.com]
synonym: "KEGG:04950" RELATED []
synonym: "MODY pathway" EXACT []
is_a: PW:0000176 ! diabetes pathway
created_by: VPetri
creation_date: 2012-07-11T12:37:25Z

[Term]
id: PW:0001039
name: Vibrio cholerae infection pathway
def: "Vibrio cholerae disease is an infection of the small intestine resulting in dehydration and electrolyte imbalance which in some cases can cause death. Cholera toxin, is one the main virulence factors of the Gram-negative Vibrio cholerae bacterium which, together with other virulence factors can invade the host." [KEGG:map05110, OneLook:http\://www.onelook.com]
synonym: "KEGG:05110" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-11T12:46:22Z

[Term]
id: PW:0001040
name: Salmonella infection pathway
def: "Salmonella, a Gram-negative bacterium of which  many species exist, in humans can cause gastroenteritis or the more severe typhoid fever. Salmonella enters the host via the digestive tract; bacteria that escape the host defense machinery can survive and replicate in Salmonella-containing vacuole (SCV) whose maturation they control." [KEGG:map05132, OneLook:http\://www.onelook.com]
synonym: "KEGG:05132" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-11T12:59:20Z

[Term]
id: PW:0001041
name: pathogenic Escherichia coli infection pathway
def: "The pathogenic Escherichia coli strains EPEC and EHEC (enteropathogenic and enterohemorrhagic E. coli, respectively) can cause sever food poisoning in humans. The non-pathogenic strains are part of the gut normal flora with beneficial contributions for the host." [KEGG:map05130, OneLook:http\://www.onelook.com]
synonym: "KEGG:05130" RELATED []
synonym: "pathogenic E. coli infection pathway" EXACT []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-11T01:23:38Z

[Term]
id: PW:0001042
name: Shigella infection pathway
def: "Shigella, a Gram-negative bacterium that is related to Salmonella and to Escherichia coli, is a disease causing agent in humans and primates. Shigellosis, also known as bacillary dysentery or Marlow syndrome is due to colonization of the intestinal epithelium and the subsequent evasion of the host defense machinery and use of host intracellular pathways by the bacteria." [KEGG:map05131, OneLook:http\://www.onelook.com]
synonym: "bacillary dysentery pathway" RELATED []
synonym: "KEGG:05131" RELATED []
synonym: "Marlow syndrome pathway" RELATED []
synonym: "Shigellosis pathway" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-11T01:44:11Z

[Term]
id: PW:0001043
name: Bordetella pertussis infection pathway
def: "The Gram-negative Bordetella pertusis Gram-negative is the causative agent of pertussis or whooping cough. One of its main virulence factors, pertussis toxin blocks the interaction of Galphai subunit of heterotrimeric G protein with its partner receptors. This results in unrestrained adenylyl cyclase activity and subsequent increased concentration of cAMP which affects normal intracellular signaling." [KEGG:map05133, OneLook:http\://www.onelook.com]
synonym: "KEGG:05133" RELATED []
synonym: "pertussis pathway" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-11T03:37:54Z

[Term]
id: PW:0001044
name: Legionella infection pathway
def: "Legionella, a pathogenic Gram-negative bacterium that includes species such as legionella pneumophila, causes several respiratory infections of which Legionnaires' disease is potentially fatal. L. pneumophila can grow within lung macrophages and is known to subvert several host pathways." [KEGG:map05134, OneLook:http\://www.onelook.com]
synonym: "KEGG:05134" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-11T04:04:16Z

[Term]
id: PW:0001045
name: Staphylococcus aureus infection pathway
def: "Staphylococcus aureus, a Gram-positive bacteria of which there are many species, usually colonizes the skin and mucous membranes of humans and other organisms and are mostly harmless. However, they can also cause a range of infections of which some can be extremely severe." [KEGG:map05150, OneLook:http\://www.onelook.com]
synonym: "KEGG:05150" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-11T04:18:10Z

[Term]
id: PW:0001046
name: Mycobacterium tuberculosis infection pathway
def: "Mycobacterium tuberculosis is the causative agent of most forms of tuberculosis. Once in the lung, they interfere with a number of intracellular pathways and processes." [KEGG:map05152, OneLook:http\://www.onelook.com]
synonym: "KEGG:05152" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-11T04:31:42Z

[Term]
id: PW:0001047
name: Leishmania infection pathway
def: "Leishmania is a protozoan parasite and a number of its species can infect mammals including humans. While the cutaneous leishmanianis is the most common form, others such as visceral or mucosal have also been reported. The infection results in alterations in a number of host signaling pathways." [KEGG:map5140, OneLook:http\://www.onelook.com]
synonym: "KEGG:05140" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-13T11:53:50Z

[Term]
id: PW:0001048
name: Trypanosoma infection pathway
def: "Trypanosoma is a protozoan parasite of which T brucei and cruzi are responsible for causing the sleeping sickness and Chagas disease, respectively. Several host signaling and regulatory pathways are altered in the infection." [KEGG:map5142, OneLook:http\://www.onelook.com]
synonym: "KEGG:5142" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-13T12:03:02Z

[Term]
id: PW:0001049
name: Trypanosoma brucei infection pathway
def: "Trypanosoma brucei, a protozoan parasite of the trypanosoma genus is the causative agent of sleeping sickness, also known as the African trypanosomias as its vector is the tsetse fly common to the sub-Saharan Africa. Several pro-inflammatory cytokines are overactivated. The neurological damage the infection causes is irreversible and the disease is fatal." [KEGG:map5143, OneLook:http\://www.onelook.com]
synonym: "African trypanosomiasis" EXACT []
synonym: "KEGG:05143" RELATED []
is_a: PW:0001048 ! Trypanosoma infection pathway
created_by: VPetri
creation_date: 2012-07-13T12:14:00Z

[Term]
id: PW:0001050
name: Trypanosoma cruzi infection pathway
def: "Trypanosoma cruzi of the genus Trypanosoma is the causative agent of the Chagas disease, also known as the American trypanosomiasis as it occurs primarily in poor areas of the Americas, mostly Central and South America. Infection interferes with a number of intracellular pathways and it appears to activate calcium signaling." [KEGG:map05142, OneLook:http\://www.onelook.com]
synonym: "American trypanosomiasis" EXACT []
synonym: "Chagas disease pathway" EXACT []
synonym: "KEGG:05142" RELATED []
is_a: PW:0001048 ! Trypanosoma infection pathway
created_by: VPetri
creation_date: 2012-07-13T12:26:45Z

[Term]
id: PW:0001051
name: Plasmodium infection pathway
def: "Plasmodium is a parasite of which several species can infect humans and cause malaria. Severe malaria, which is primarily caused by Plasmodium falciparum, can lead to death and the fatalities are mostly children. Deregulated induction of cytokines appears to play a role in the infection." [KEGG:map05144]
synonym: "KEGG:05144" RELATED []
synonym: "malaria infection pathway" EXACT []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-13T12:36:12Z

[Term]
id: PW:0001052
name: Toxoplasma gondii infection pathway
def: "Toxoplasma gondii whose host includes various warm-blooded species including humans, is the causative agent of toxoplasmosis. The infection interferes with a number of host pathways; in its most severe manifestations it can be fatal." [KEGG:map05145, OneLook:http\://www.onelook.com]
synonym: "KEGG:05145" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-13T01:00:51Z

[Term]
id: PW:0001053
name: Entamoeba histolyca infection pathway
def: "Entamoeba histolyca is a prozoan parasite that is the causative agent of amoebiasis which affects the intestinal tissue leading to severe dysentery and ulcerations. It can also infect other tissues such as the liver to a lesser extent the brain, lungs and spleen." [KEGG:map5146, OneLook:http\://www.onelook.com]
synonym: "amoebiasis infection pathway" EXACT []
synonym: "KEGG:05146" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-13T01:13:24Z

[Term]
id: PW:0001054
name: influenza A virus infection pathway
def: "Influenza A virus is the causative agent of seasonal epidemics and occasional  pandemics of influenza which affects the respiratory system." [KEGG:map05164]
synonym: "KEGG:05164" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-13T01:21:37Z

[Term]
id: PW:0001055
name: hepatitis C virus infection pathway
def: "Hepatitis C virus is the causative agent of hepatitis C, a chronic liver disease in humans. The virus interferes with several signaling and regulatory pathways in the host cells." [KEGG:map05160, OneLook:http\://www.onelook.com]
synonym: "KEGG:05160" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-13T01:22:51Z

[Term]
id: PW:0001056
name: Herpes simplex virus infection pathway
synonym: "KEGG:05168" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-16T01:24:16Z

[Term]
id: PW:0001057
name: Epstein-Barr virus infection pathway
synonym: "KEGG:05169" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-16T01:26:38Z

[Term]
id: PW:0001058
name: measles infection pathway
def: "Measles virus (MV) of the genus Morbilivirus is the causative agent of the condition that bears its name. The condition causes immunosuppression and several MV proteins are thought to interfere with the normal host immune responses." [KEGG:map05162, OneLook:http\://wwwonelook.com]
synonym: "KEGG:05162" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-07-16T01:37:38Z

[Term]
id: PW:0001059
name: oxidative phosphorylation pathway
def: "Oxidative phosphorylation is the coupling of the electron transport chain and the ATP biosynthetic pathways. The electron transfer chain generates an electrochemical gradient that drives the phosphorylation of ADP. Under certain circumstances the two may be uncoupled." [GO:0006119, KEGG:map00190, PMID:19760284, PMID:21625217]
synonym: "KEGG:00190" RELATED []
is_a: PW:0000033 ! energy metabolic pathway
created_by: VPetri
creation_date: 2012-07-18T09:38:02Z

[Term]
id: PW:0001060
name: primary bile acid biosynthetic pathway
def: "Primary bile acids, cholic and  chenodeoxycholic acids, are derived from cholesterol in the liver. Upon conjugation with glycine or taurine they can be secreted into the intestine." [KEGG:map00120, OneLook:http\://www.onelook.com]
synonym: "KEGG:00120" RELATED []
is_a: PW:0000039 ! bile acid biosynthetic pathway
created_by: VPetri
creation_date: 2012-07-18T10:47:50Z

[Term]
id: PW:0001061
name: secondary bile acid biosynthetic pathway
def: "Secondary bile acids, deoxycholic and lithocholic acids, are synthesized from the primary ones by intestinal bacteria. like the primary bile acids, they need to be conjugated to glycine or taurine prior to secretion." [KEGG:map00121, OneLook:http\://www.onelook.com]
is_a: PW:0000039 ! bile acid biosynthetic pathway
created_by: VPetri
creation_date: 2012-07-18T10:54:59Z

[Term]
id: PW:0001062
name: lacto-series glycosphingolipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of lacto-series type of glycosphingolipids." [PMID:1 7976918]
synonym: "KEGG:00601" RELATED []
is_a: PW:0000733 ! glycosphingolipid metabolic pathway
created_by: VPetri
creation_date: 2012-07-19T01:18:59Z

[Term]
id: PW:0001063
name: lipoic acid metabolic pathway
def: "The metabolic reactions involving lipoic acid, a compound derived from octanoic acid that contains two sulfur centers. Lipoic acid is a co-factor for the pyruvate dehydrogenase complex responsible for the irreversible decarboxylation of pyruvate to acetyl-CoA." [KEGG:map00785, OneLook:http\://www.onelook.com, PMID:17052205]
synonym: "KEGG:00785" RELATED []
is_a: PW:0000135 ! metabolic pathway of cofactors, vitamins, nutrients
created_by: VPetri
creation_date: 2012-07-19T01:37:53Z

[Term]
id: PW:0001064
name: phosphonate and phosphinate metabolic pathway
def: "Those metabolic reactions involving phosphonate and phosphinate, organic compounds that contain carbon-phosphorus bonds and which can be synthesized by bacteria and protists." [KEGG:mapp00440]
is_a: PW:0000132 ! metabolic pathway of other amino acids
created_by: VPetri
creation_date: 2012-07-23T03:43:37Z

[Term]
id: PW:0001065
name: interstrand cross link repair pathway
def: "Interstrand cross links (ICL) of DNA can be induced by both endogenous and exogenous ligands. ICL if not repaired will lead to cell death. ICL repair pathway, also known as Fanconi anemia pathway is the cellular response to this type of DNA damage." [PMID:19061902, PMID:20713514, PMID:21605559]
synonym: "Fanconi anemia pathway" EXACT []
synonym: "ICL repair pathway" EXACT []
synonym: "KEGG:03460" RELATED []
is_a: PW:0000663 ! double-strand DNA repair pathway
created_by: VPetri
creation_date: 2012-07-24T09:31:12Z

[Term]
id: PW:0001066
name: ribosome biogenesis pathway
def: "The pathway of ribosome biogenesis underlies the production of ribosomal RNAs, of core ribosomal and associated proteins and of small nucleolar RNAs along with their accurate assembly into the mature ribosome. It starts in the nucleolus with the final assembly and maturation steps in the cytoplasm. Alterations in the pathway result in specific phenotypes collectively known as ribosomopathies." [PMID:20194897, PMID:20875629]
synonym: "KEGG:03008" RELATED []
relationship: part_of PW:0000101 ! translation pathway
created_by: VPetri
creation_date: 2012-07-25T03:15:38Z

[Term]
id: PW:0001067
name: altered ribosome biogenesis pathway
def: "Alterations in the pathway result in specific phenotypes collectively known as ribosomopathies." [PMID:20194897]
is_a: PW:0001066 ! ribosome biogenesis pathway
is_a: PW:0001068 ! altered translation pathway
created_by: VPetri
creation_date: 2012-07-25T04:19:34Z

[Term]
id: PW:0001068
name: altered translation pathway
is_a: PW:0000101 ! translation pathway
is_a: PW:0000290 ! altered pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
created_by: VPetri
creation_date: 2012-07-25T04:21:04Z

[Term]
id: PW:0001069
name: gonadotropin-releasing hormone signaling pathway
def: "Gonadotropin-releasing hormone signaling pathway induces the synthesis and secretion of luteinizing and follicle-stimulating hormones from the pituitary." [PMID:22024993]
synonym: "GnRH signaling pathway" EXACT []
synonym: "KEGG:04912" RELATED []
synonym: "luteinizing hormone-releasing hormone signaling pathway" RELATED []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2012-07-30T11:02:37Z

[Term]
id: PW:0001070
name: luteinizing hormone signaling pathway
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2012-07-30T11:12:02Z

[Term]
id: PW:0001071
name: follicle-stimulating hormone signaling pathway
def: "Follicle-stimulating hormone signaling is important for the normal development and function of the ovaries and testes." [PMID:21372710]
synonym: "FSH signaling pathway" EXACT []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2012-07-30T11:13:34Z

[Term]
id: PW:0001072
name: synaptic vesicle cycle pathway
def: "The cycle of synaptic vesicle exocytosis and neurotransmitter release and the subsequent endocytosis and recycling of synaptic vesicles at nerve terminals." [PMID:15217342]
synonym: "KEGG:04721" RELATED []
relationship: part_of PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse
created_by: VPetri
creation_date: 2012-07-30T03:31:02Z

[Term]
id: PW:0001073
name: spliceosome pathway
def: "The spliceosome is a multimegadalton ribonucleoprotein complex that removes the exons to produce the mature mRNA, including several mature mRNAs from a single RNA transcript via alternative splicing. A complex assembly/disassembly  pathway mediates the two chemical steps of a splicing event." [PMID:21441581, PMID:22010274, PMID:22480731, PMID:22975042]
synonym: "KEGG:03040" RELATED []
relationship: part_of PW:0000127 ! RNA polymerase II transcription pathway
created_by: VPetri
creation_date: 2012-07-31T09:43:57Z

[Term]
id: PW:0001074
name: hydrophobic amino acid metabolic pathway
def: "Those metabolic reactions involving hydrophobic, uncharged amino acids. Hydrophobic amino acids include alanine, valine, isoleucine, leucine and methionine with hydrocarbon side chains and the phenylalanine, tyrosine and tryptophan with bulky, aromatic side chains." [MCE library:Handbooks of biochemistry]
is_a: PW:0000011 ! amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T10:30:19Z

[Term]
id: PW:0001075
name: hydrophilic amino acid metabolic pathway
def: "Those metabolic reactions involving hydrophilic, polar amino acids. The hydrophilic amino acids include the negatively charged (acidic) aspartic acid and glutamic acid whose salts are glutamate and aspartate, respectively, the positively charged (basic) lysine and arginine and the uncharged polar asparagine, cysteine, glutamine, serine and threonine. Histidine, whose side chain contains an imidazole can shift from positively charged to neutral." [MCW library:Handbooks of biochemistry]
is_a: PW:0000011 ! amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T10:39:29Z

[Term]
id: PW:0001076
name: special amino acid metabolic pathway
def: "Those metabolic reactions involving special amino acids. The special amino acids include cysteine whose side chain contains a sulfhydryl group, glycine whose side chain is a hydrogen atom and proline whose side chain bends to form a ring and hose rigidity limits the folding abilities of proteins around proline residues." [MCW library:Nahdbooks of biochemistry]
is_obsolete: true
created_by: VPetri
creation_date: 2012-07-31T10:47:08Z

[Term]
id: PW:0001077
name: amino acid metabolic pathway (KEGG)
def: "Those metabolic reactions involving amino acids as listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG)." [KEGG:http\://www.genome.jp/kegg/]
is_a: PW:0000011 ! amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T10:56:10Z

[Term]
id: PW:0001078
name: cysteine and methionine metabolic pathway
synonym: "KEGG:00270" RELATED []
is_a: PW:0001077 ! amino acid metabolic pathway (KEGG)
created_by: VPetri
creation_date: 2012-07-31T11:04:19Z

[Term]
id: PW:0001079
name: proline metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of proline, a non-essential amino acid that could be essential in certain cases. Its side chain bends to form a ring and its rigidity limits the folding abilities of proteins around proline residues." [OneLook:http\://www.onelook.com]
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:05:36Z

[Term]
id: PW:0001080
name: valine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of valine, an essential amino acid. Valine, along with leucine and isoleucine is a branched-chain amino acid." [wikipedia:http\://en.wikipedia.org/wiki/Valine]
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:06:01Z

[Term]
id: PW:0001081
name: lysine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of lysine, an essential amino acid." [OneLook:http\://www.onelook.com]
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:07:54Z

[Term]
id: PW:0001082
name: arginine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of arginine, a non-essential amino acid that could be essential in certain cases." [OneLook:http\://www.onelook.com]
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:08:11Z

[Term]
id: PW:0001083
name: asparagine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of asparagine, a non-essential amino acid." [OneLook:http\://www.onelook.com]
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:08:57Z

[Term]
id: PW:0001084
name: serine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of serine, a non-essential amino acid that could be essential in certain cases." [OneLook:http\://www.onelook.com]
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:10:13Z

[Term]
id: PW:0001085
name: threonine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of threonine, an essential amino acid." [OneLook:http\://www.onelook.com]
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:11:19Z

[Term]
id: PW:0001086
name: glutamine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glutamine, a non-essential amino acid that could be essential in certain cases." [OneLook:http\://www.onelook.com]
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:12:05Z

[Term]
id: PW:0001087
name: isoleucine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of isoleucine, an essential amino acid." [OneLook:http\://www.onelook.com]
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:18:29Z

[Term]
id: PW:0001088
name: leucine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of leucine, an essential amino acid." [OneLook:http\://www.onelook.com]
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
created_by: VPetri
creation_date: 2012-07-31T11:18:56Z

[Term]
id: PW:0001089
name: serotonin signaling pathway via receptors engaging G alphai protein family
def: "Serotonin signaling via receptor family 1 and 5 primarily engages G alphai protein family resulting in inhibition of adenylate cyclases and reduction of intracellular cAMP. There are five receptors subtypes in family 1 and one in the human family 5." [PMID:20945968]
is_a: PW:0000854 ! serotonin signaling pathway
created_by: VPetri
creation_date: 2012-08-01T03:14:20Z

[Term]
id: PW:0001090
name: serotonin signaling pathway via receptors engaging G alphaq protein family
def: "Serotonin signaling via receptor family 2 engages G alphaq protein family resulting in activation of phospholipase C, mobilization of calcium ions and production of inositol 1,4,5-triphosphate (IP3) and diacylglycerol (DAG). There are three receptors subtypes in family 2." [PMID:20945968]
is_a: PW:0000854 ! serotonin signaling pathway
created_by: VPetri
creation_date: 2012-08-01T03:20:07Z

[Term]
id: PW:0001091
name: serotonin signaling pathway via receptors engaging G alphas protein family
def: "Serotonin signaling via receptor family 4, 6, and 7 engages G alphas protein family resulting in activation of adenylyl cyclases and increased concentration of cAMP. There are seven receptor subtypes in family 4 and only one in families 6 and 7." [PMID:20945968]
is_a: PW:0000854 ! serotonin signaling pathway
created_by: VPetri
creation_date: 2012-08-01T03:28:58Z

[Term]
id: PW:0001092
name: serotonin signaling via receptor family 3
def: "Serotonin family 3 receptor is a ligand-gated Na+/K+ channel with two receptor subtypes and their heterodimerization is believed to be necessary for their function. Serotonin signaling results in depolarization of plasma membrane." [PMID:20945968]
is_a: PW:0000854 ! serotonin signaling pathway
created_by: VPetri
creation_date: 2012-08-01T03:33:01Z

[Term]
id: PW:0001093
name: bile acid signaling pathway
def: "Bile acid binds to and activates several nuclear receptors such as the farnesoid X and liver X receptors as well as a cell surface G-protein coupled receptor." [PMID:22414897, PMID:22521118]
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0000959 ! lipid signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2012-08-03T10:23:51Z

[Term]
id: PW:0001094
name: altered estrogen signaling pathway
def: "Disregulated estrogen signaling is associated with the growth and development of breast cancers; estrogen mediated transcription is constitutively active in more than 50% of cases." [PMID:9608332]
is_a: PW:0000507 ! estrogen signaling pathway
is_a: PW:0000719 ! altered transcription factor mediated signaling pathway
is_a: PW:0000787 ! altered sex steroids signaling pathway
is_a: PW:0001314 ! altered transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2012-08-03T10:51:00Z

[Term]
id: PW:0001095
name: zidovudine drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of zidovudine, an anti-viral drug used for the treatment of HIV infection. It belongs to the family of nucleoside analog reverse transcriptase inhibitors." [PharmGKB:http\://www.pharmgkb.org]
synonym: "ZDV drug pathway" RELATED []
is_a: PW:0000996 ! anti-infective drug pathway
created_by: VPetri
creation_date: 2012-08-03T11:18:59Z

[Term]
id: PW:0001096
name: zidovudine pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of zidovudine, a drug used for the treatment of HIV. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org]
is_a: PW:0001095 ! zidovudine drug pathway
created_by: VPetri
creation_date: 2012-08-03T11:23:05Z

[Term]
id: PW:0001097
name: zidovudine pharmacodynamics pathway
def: "The pathway of zidovudine-target interaction and of the biochemical or physiological responses to them. Zidovudine is a drug used for the treatment of HIV infection. Zidovudine, in its active triphosphate form, inhibits HIV-1 reverse transcriptase activity. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:www.pharmgkb.org]
is_a: PW:0001095 ! zidovudine drug pathway
created_by: VPetri
creation_date: 2012-08-03T11:25:55Z

[Term]
id: PW:0001098
name: tramadol drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of tramadol, an analgesic used for the treatment of moderate to moderately severe pain. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [OneLook:http\://www.onelook.com, PharmGKB:http\://www.pharmgkb.org]
is_a: PW:0000923 ! nervous system drug pathway
created_by: VPetri
creation_date: 2012-08-03T11:37:59Z

[Term]
id: PW:0001099
name: tramadol pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of tramadol, an analgesic used in the treatment of pain. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.onelook.com]
is_a: PW:0001098 ! tramadol drug pathway
created_by: VPetri
creation_date: 2012-08-03T11:41:01Z

[Term]
id: PW:0001100
name: tramadol pharmacodynamics pathway
def: "The pathway of tramadol-target interaction and of the biochemical or physiological responses to drug. Tramadol is an analgesic used for the treatment of pain. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org]
is_a: PW:0001098 ! tramadol drug pathway
created_by: VPetri
creation_date: 2012-08-03T11:41:20Z

[Term]
id: PW:0001101
name: viral carcinogenesis pathway
def: "A number of human viruses have been shown to be associated/contribute to approximately 10 to 15% of cancers. The viral particles encode oncogenes whose escape from the host defense system impacts on many cellular pathways and promotes tumor development." [OneLook:http\://www.onelook.com, PMID:20971551, PMID:21102637, PMID:21445966]
synonym: "KEGG:05203" RELATED []
is_a: PW:0000605 ! cancer pathway
created_by: VPetri
creation_date: 2012-09-06T16:03:33Z

[Term]
id: PW:0001102
name: altered hypoxia inducible factor pathway
def: "A hypoxia inducible pathway that deviates from what its normal course should be. Mutations in the von Hippel-Lindau (Vhl), the E3 ubiquitin ligase which targets Hif alpha for degradation under normoxic conditions, lead to a constitutively active pathway regardless the levels of oxygen. Mutations in Vhl and a number of other genes have been implicated in renal cancers." [PMID:22406000]
is_a: PW:0000360 ! hypoxia inducible factor pathway
is_a: PW:0000361 ! altered oxygen homeostasis pathway
is_a: PW:0000719 ! altered transcription factor mediated signaling pathway
is_a: PW:0001314 ! altered transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2012-10-04T11:04:37Z

[Term]
id: PW:0001103
name: acid-base homeostasis pathway
def: "The pathways that respond to and control the levels of protons, bicarbonate and carbon dioxide and of ammonia the cells. Several sensing pathways, i.e., prompting intracellular signaling cascade, and transport have been identified as critical players. The kidneys play a major role along with the respiratory system." [PMID:22362904]
is_a: PW:0000355 ! homeostasis pathway
created_by: VPetri
creation_date: 2012-10-04T12:58:08Z

[Term]
id: PW:0001104
name: pH sensing signaling pathway
def: "The pathway that respond to increases or decreases in protons, or pH levels and whose signaling aim at restoring systemic acid-base balance. Several G-protein coupled receptor  (GPCRs) and ion channel mediated signaling have been reported in the literature." [PMID:20683624]
synonym: "proton-activated signaling pathway" RELATED []
is_a: PW:0001105 ! acid and base sensing signaling pathway
relationship: part_of PW:0001103 ! acid-base homeostasis pathway
created_by: VPetri
creation_date: 2012-10-04T13:14:56Z

[Term]
id: PW:0001105
name: acid and base sensing signaling pathway
def: "The signaling pathway elicited by changes in pH and bicarbonate levels." [PMID:20683624]
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2012-10-04T13:39:02Z

[Term]
id: PW:0001106
name: bicarbonate sensing signaling pathway
def: "The signaling pathway elicited by increased levels of bicarbonate. Bicarbonate results from the instantaneous dissociation of carbonic acid, the end product of carbonic anhydrase hydration of exogenous or metabolically produced carbon dioxide." [PMID:20683624]
is_a: PW:0001105 ! acid and base sensing signaling pathway
relationship: part_of PW:0001103 ! acid-base homeostasis pathway
created_by: VPetri
creation_date: 2012-10-04T13:43:43Z

[Term]
id: PW:0001107
name: sorafenib drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of sorafenib, a multikinase inhibitor used in the treatment of cancer, in particular for advanced renal cell carcinoma.  The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:21419641, PMID:22263843]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-10-04T15:24:58Z

[Term]
id: PW:0001108
name: sorafenib pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of sorafenib. The drug was the first oral multikinase inhibitor approved for the treatment of renal cell carcinoma. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165959537, PMID:21419641]
is_a: PW:0001107 ! sorafenib drug pathway
created_by: VPetri
creation_date: 2012-10-04T15:30:52Z

[Term]
id: PW:0001109
name: sorafenib pharmacodynamics pathway
def: "The pathway of sorafenib-target interaction and of the biochemical or physiological responses to drug. Sorafenib is the first multikinase inhibitor approved for the treatment of renal cell carcinoma.  The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165959584, PMID:21419641]
is_a: PW:0001107 ! sorafenib drug pathway
created_by: VPetri
creation_date: 2012-10-04T15:31:17Z

[Term]
id: PW:0001110
name: sunitinib drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of sunitinib, a multikinase inhibitor used in the treatment of cancer, in particular for advanced renal cell carcinoma. The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:22328304]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-10-04T15:54:48Z

[Term]
id: PW:0001111
name: tocilizumab pharmacokinetics pathway
is_a: PW:0000928 ! tocilizumab drug pathway
created_by: VPetri
creation_date: 2012-10-04T15:57:07Z

[Term]
id: PW:0001112
name: tocilizumab pharmacodynamics pathway
is_a: PW:0000928 ! tocilizumab drug pathway
created_by: VPetri
creation_date: 2012-10-04T15:57:36Z

[Term]
id: PW:0001113
name: sunitinib pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of sunitinib. The drug is a multikinase inhibitor approved for the treatment of renal cell carcinoma. Genetic variations can result in changes in the availability of the drug." [PMID:22328304]
is_a: PW:0001110 ! sunitinib drug pathway
created_by: VPetri
creation_date: 2012-10-04T15:58:20Z

[Term]
id: PW:0001114
name: sunitinib pharmacodynamics pathway
def: "The pathway of sunitinib-target interaction and of the biochemical or physiological responses to drug. Sunitinib is a multikinase inhibitor approved for the treatment of renal cell carcinoma. The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can cause differences in the response of the organism to the drug." [PMID:2232830]
is_a: PW:0001110 ! sunitinib drug pathway
created_by: VPetri
creation_date: 2012-10-04T15:58:42Z

[Term]
id: PW:0001115
name: non-visual phototransduction pathway
def: "A signaling cascade triggered by light in the visible and red spectrum whose sensor appears to be cytochrome c oxidase, the terminal enzyme of the electron transfer chain, and which relies on a retrograde mitochondrion-to-nucleus pathway that translates in the upregulation of various genes. Unlike the visual phototransduction, this pathway does not require vitamin A metabolites." [PMID:20681024]
is_a: PW:0001008 ! photosignal transduction pathway
created_by: VPetri
creation_date: 2012-10-11T09:27:12Z

[Term]
id: PW:0001116
name: vitamin A and metabolites signaling pathway
is_a: PW:0001012 ! vitamin and vitamin metabolites signaling pathway
created_by: VPetri
creation_date: 2012-10-11T10:05:25Z

[Term]
id: PW:0001117
name: retinol mediated signaling pathway
def: "A signaling pathway mediated by a signaling complex for which retinol or vitamin A appears to be an essential docking molecule and redox sensor. The pathway may play an important role in regulating the tricarboxylic acid cycle through the pyruvate dehydrogenase complex by mechanisms that are still to be elucidated." [PMID:21763457]
is_a: PW:0001116 ! vitamin A and metabolites signaling pathway
created_by: VPetri
creation_date: 2012-10-11T10:06:06Z

[Term]
id: PW:0001118
name: altered energy metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway
created_by: VPetri
creation_date: 2012-10-12T16:31:32Z

[Term]
id: PW:0001119
name: altered citric acid cycle pathway
def: "Defects in components of the citrate cycle have been shown to relate to several types of cancer. For instance, mutations in fumarate hydratase are associated with renal cancer, in succinate dehydrogenase in renal as well as paragangliomas and pheochromocytomas. Mutations in isocitrate dehydrogenase have also been implicated in several types of cancer. Defects in this central metabolic network result in unwanted activation of hypoxia inducible factor whose target genes are involved in angiogenesis, erythropoiesis, glycolysis, among others." [PMID:21764377, PMID:23001348]
is_a: PW:0000026 ! citric acid cycle pathway
is_a: PW:0000359 ! altered energy homeostasis pathway
is_a: PW:0001118 ! altered energy metabolic pathway
created_by: VPetri
creation_date: 2012-10-12T16:32:05Z

[Term]
id: PW:0001120
name: bevacizumab drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of bevacizumab, a humanized monoclonal antibody that inhibits VEGF activity. It is used for the treatment of several types of advanced cancers. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:22594892]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-10-15T08:49:28Z

[Term]
id: PW:0001121
name: bevacizumab pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of bevacizumab, a VEGF inhibitor used in the treatment of several types of  tumors. Genetic variations can result in changes in the availability of the drug." [PMID:22594892\:]
is_a: PW:0001120 ! bevacizumab drug pathway
created_by: VPetri
creation_date: 2012-10-15T08:56:41Z

[Term]
id: PW:0001122
name: bevacizumab pharmacodynamics pathway
def: "The pathway of bevacizumab-target interaction and of the biochemical or physiological responses to drug. The drug is an inhibitor of VEGF and is used in the treatment of several types of cancers such as for instance renal cell carcinoma. VEGF is a target of hypoxia inducible factor pathway, which is constitutively active in the condition.  Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:22594892]
is_a: PW:0001120 ! bevacizumab drug pathway
created_by: VPetri
creation_date: 2012-10-15T08:57:45Z

[Term]
id: PW:0001123
name: axitinib drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of axitinib, a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma as well as other tumors. Angiogenic factors such as vascular endothelial or platelet derived growth factors are direct and indirect targets of hypoxia inducible factor pathway, constitutively active in renal cell carcinoma. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:22170007]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-10-19T11:46:54Z

[Term]
id: PW:0001124
name: axitinib pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of axitinib, a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma and other tumors. Axitinib is a selective second generation inhibitor of vascular endothelial growth factor receptors 1, 2 and 3. Genetic variations can result in changes in the availability of the drug." [PMID:22170007]
is_a: PW:0001123 ! axitinib drug pathway
created_by: VPetri
creation_date: 2012-10-19T11:49:57Z

[Term]
id: PW:0001125
name: axitinib pharmacodynamics pathway
def: "The pathway of axitinib-target interaction and of the biochemical or physiological responses to drug. Axitinib is a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma as well as other tumors. Axitinib is a selective second generation inhibitor of vascular endothelial growth factor receptors 1, 2 and 3. Genetic variations can cause differences in the response of the organism to the drug." [PMID:22170007]
is_a: PW:0001123 ! axitinib drug pathway
created_by: VPetri
creation_date: 2012-10-19T11:50:16Z

[Term]
id: PW:0001126
name: everolimus drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of everolimus, an inhibitor of mTOR pathway used in the treatment of several types of tumors, including renal cell carcinoma. Hypoxia inducible factor (HIF) pathway is constitutively active in the disease; mTOR regulates the translation of HIF-alpha gene. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:20456985]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-10-19T13:54:12Z

[Term]
id: PW:0001127
name: everolimus pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of everolimus, an inhibitor of mTOR pathway used in the treatment of renal cell carcinoma and other tumors. Genetic variations can result in changes in the availability of the drug." [PMID:20456985, PMID:22624503]
is_a: PW:0001126 ! everolimus drug pathway
created_by: VPetri
creation_date: 2012-10-19T15:41:34Z

[Term]
id: PW:0001128
name: everolimus pharmacodynamics pathway
def: "The pathway of everolimus-target interactions and of the biochemical or physiological responses to drug. The drug is an inhibitor of mTOR pathway and is used in the treatment of renal cell carcinoma and other types of tumors. Genetic variations can cause differences in the response of the organism to the drug." [PMID:20456985]
is_a: PW:0001126 ! everolimus drug pathway
created_by: VPetri
creation_date: 2012-10-19T15:45:06Z

[Term]
id: PW:0001129
name: temsirolimus drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of temsirolimus, an inhibitor of mTOR pathway used in the treatment of renal cell carcinoma and other types of tumors. Hypoxia inducible factor (HIF) pathway is constitutively active in renal cell carcinoma; HIF-alpha translation is under the control of mTOR pathway. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:20456985]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-10-19T16:04:14Z

[Term]
id: PW:0001130
name: temsirolimus pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of temsirolimus, an inhibitor of mTOR pathway used in the treatment of renal cell carcinoma and other tumors. Genetic variations can result in changes in the availability of the drug." [PMID:20456985]
is_a: PW:0001129 ! temsirolimus drug pathway
created_by: VPetri
creation_date: 2012-10-19T16:12:25Z

[Term]
id: PW:0001131
name: temsirolimus pharmacodynamics pathway
def: "The pathway of temsirolimus-target interaction and of the biochemical or physiological responses to drug. The drug is an inhibitor of mTOR pathway and is used in the treatment of renal cell carcinoma and other types of tumors. Genetic variations can cause differences in the response of the organism to the drug." [PMID:20456985]
is_a: PW:0001129 ! temsirolimus drug pathway
created_by: VPetri
creation_date: 2012-10-19T16:12:49Z

[Term]
id: PW:0001132
name: pazopanib drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of pazopanib, a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma as well as other tumors. Angiogenic factors such as vascular endothelial or platelet derived growth factors are direct and indirect targets of hypoxia inducible factor pathway, constitutively active in renal cell carcinoma. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:20456985]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2012-10-19T16:13:35Z

[Term]
id: PW:0001133
name: pazopanib pharmacokinetics pathway
def: "he pathway of processing - absorption, distribution, metabolism or elimination - of pazopanib. The drug is a multikinase inhibitor approved for the treatment of renal cell carcinoma. Genetic variations can result in changes in the availability of the drug." [PMID:20456985]
is_a: PW:0001132 ! pazopanib drug pathway
created_by: VPetri
creation_date: 2012-10-19T16:13:55Z

[Term]
id: PW:0001134
name: pazopanib pharmacodynamics pathway
def: "The pathway of pazopanib-target interaction and of the biochemical or physiological responses to drug. Pazopanib is a selective multikinase inhibitor approved for the treatment or renal cell carcinoma. The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can cause differences in the response of the organism to the drug." [PMID:20456985]
is_a: PW:0001132 ! pazopanib drug pathway
created_by: VPetri
creation_date: 2012-10-19T16:14:15Z

[Term]
id: PW:0001135
name: parathyroid hormone signaling pathway
def: "Parathyroid hormone (PTH) signaling is important for calcium and phosphate homeostasis in bone and kidney. It acts to increase the concentration of calcium in the blood, has both anabolic and catabolic effects in the bone and regulates calcium and phosphate reabsorption in the kidney. It also plays important roles in vitamin D metabolism." [PMID:19857544, PMID:21777186, PMID:23060860]
synonym: "PTH signaling pathway" RELATED []
is_a: PW:0001180 ! parathyroid hormone family signaling pathway
relationship: part_of PW:0000371 ! calcium homeostasis pathway
relationship: part_of PW:0001182 ! phosphate homeostasis pathway
created_by: VPetri
creation_date: 2012-11-01T09:32:46Z

[Term]
id: PW:0001136
name: fatty acid elongation pathway
def: "The C16 palmitate product of fatty acid biosynthetic pathway can be esterifed to triacylglycerol or converted to longer chain saturated and unsaturated fatty acid molecules by elongases and desaturases, depending on the needs of the cell. The elongation pathway takes place in the endoplasmic reticulum or in the mitochondrion. Longer chain fatty acids are present in certain specialized tissues; for instance, myelin contains large amounts of C22 and C24 molecules." [KEGG:map00062]
synonym: "KEGG:00062" RELATED []
is_a: PW:0000058 ! fatty acid metabolic pathway
created_by: VPetri
creation_date: 2012-11-02T15:26:41Z

[Term]
id: PW:0001137
name: unsaturated fatty acid biosynthetic pathway
def: "The C16 palmitate product of fatty acid biosynthetic pathway can be esterifed to triacylglycerol or converted to longer chain saturated and unsaturated fatty acid molecules by elongases and desaturases, depending on the needs of the cell. Unsaturated fatty acids are essential membrane components." [KEGG:map01040]
synonym: "KEGG:01040" RELATED []
is_a: PW:0000058 ! fatty acid metabolic pathway
created_by: VPetri
creation_date: 2012-11-02T15:40:42Z

[Term]
id: PW:0001138
name: ether lipid metabolic pathway
def: "Those metabolic reactions involving ether lipids, lipid molecules in which one or several of the carbons on glycerol has an ether linkage to an alkyl chain. Ether lipids are constituents of cell membrane; some metabolites could act as signaling second messengers or carry out antioxidant functions." [KEGG:map00565, OneLook:http\://www.onelook.com]
synonym: "KEGG:00565" RELATED []
is_a: PW:0001137 ! unsaturated fatty acid biosynthetic pathway
created_by: VPetri
creation_date: 2012-11-02T16:17:56Z

[Term]
id: PW:0001139
name: calcium transport pathway
def: "Calcium is pumped into organelles or outside the cell by pumps and exchangers to maintain the low calcium concentration necessary for cell viability. Many type of channels, some calcium-selective, others of lower selectivity or calcium-permeant, allow for the flow of calcium from external sources or internal stores into the cell to initiate many signaling events. The movement of calcium ions, which controls and maintains the calcium gradient, and calcium signaling, which the gradient promotes, are inextricably connected in the fabric of calcium homeostasis." [PMID:12838335, PMID:18083096]
is_a: PW:0000593 ! metal ion transport pathway
relationship: part_of PW:0000371 ! calcium homeostasis pathway
created_by: VPetri
creation_date: 2012-11-05T09:59:28Z

[Term]
id: PW:0001140
name: calcium/calcium-mediated signaling pathway
def: "Calcium signaling impacts on a large and diverse spectrum of cellular processes such as gene expression and cell death, proliferation, muscle contraction and energy metabolism, learning, memory and synaptic plasticity. Calcium acts in signal transduction as a first as well as a second messenger. Calcium transport, which controls and maintains the calcium gradient, and calcium signaling, which the gradient promotes, are inextricably connected in the fabric of calcium homeostasis." [PMID:12838335, PMID:17574670, PMID:18083096, PMID:19243429]
synonym: "KEGG:04020" RELATED []
is_a: PW:0000003 ! signaling pathway
relationship: part_of PW:0000371 ! calcium homeostasis pathway
created_by: VPetri
creation_date: 2012-11-05T10:53:28Z

[Term]
id: PW:0001141
name: calcium signaling pathway via the calcium-sensing receptor
def: "Calcium signaling through the calcium-sensing receptor inhibits the secretion of parathyroid hormone in the parathyroid glands and controls calcium absorption and water balance in the kidneys. Calcium is considered the main physiological agonist but other cations and various agonists can activate the receptor. The G protein coupled receptor (GPCR) is believed to engage several types of Galpha proteins and to have many other interacting partners. The pathway leads to activation of MAPK cascades, particularly the one mediated by Erk1/2. Casr signaling is cell specific; many of its molecular details are not fully understood. Many mutations, both inactivating and activating the receptor, have been identified." [PMID:20729338]
is_a: PW:0001140 ! calcium/calcium-mediated signaling pathway
created_by: VPetri
creation_date: 2012-11-07T13:22:52Z

[Term]
id: PW:0001142
name: clathrin-mediated endocytosis pathway
def: "The clathrin-mediated endocytosis pathway involves clathrin-coated vesicles used for the engulfment of material." [PMID:16985500, Wikipedia:http\://en.wikipedia.org/wiki/Endocytosis]
is_a: PW:0000281 ! endocytosis pathway
created_by: VPetri
creation_date: 2012-11-08T15:18:18Z

[Term]
id: PW:0001143
name: caveolae-mediated endocytosis pathway
is_a: PW:0000281 ! endocytosis pathway
created_by: VPetri
creation_date: 2012-11-08T15:40:59Z

[Term]
id: PW:0001144
name: micropinocytosis pathway
is_a: PW:0000281 ! endocytosis pathway
created_by: VPetri
creation_date: 2012-11-08T15:41:28Z

[Term]
id: PW:0001145
name: phagocytosis pathway
def: "Phagocytosis pathway is used for the removal of unwanted material such as dying cells and also of foreign material. As such is also part of the immune response. Various receptors on the surface of a phagocytic cell will recognize/bind material and induce signaling cascades." [PMID:16985500, PMID:9039775]
synonym: "KEGG:04145" RELATED []
is_a: PW:0000281 ! endocytosis pathway
created_by: VPetri
creation_date: 2012-11-08T15:41:47Z

[Term]
id: PW:0001146
name: Fc gamma receptor mediated signaling pathway
def: "The signaling cascade initiated by an activated Fc gamma receptor. Fc receptors are classified by the type of antibody they recognize; thus, Fc gamma receptors bind IgG, the most common type of antibody. Fc gamma receptors belong to the immunoglobulin superfamily." [PMID:15466916]
synonym: "KEGG:04666" RELATED []
is_a: PW:0001145 ! phagocytosis pathway
is_a: PW:0001150 ! Fc receptor mediated signaling pathway
created_by: VPetri
creation_date: 2012-11-08T16:04:35Z

[Term]
id: PW:0001147
name: eicosanoid signaling pathway via peroxisome proliferator-activated receptor gamma
synonym: "eicosanoid signaling pathway via PPARG" EXACT []
synonym: "KEGG:03320" RELATED []
is_a: PW:0000565 ! eicosanoid signaling pathway
created_by: VPetri
creation_date: 2012-11-08T16:29:11Z

[Term]
id: PW:0001148
name: hepatitis B virus infection pathway
def: "Hepatitis B virus (HBV) is the causative agent of hepatitis B, an inflammatory condition of the liver affecting people in parts of Asia and Africa. The virus interferes with a number of regulatory and signaling pathways in the host." [Wikipedia:http\://en.wikipedia.org/wiki/Hepatitis_B]
synonym: "KEGG:05161" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-11-09T08:47:08Z

[Term]
id: PW:0001149
name: human T-lymphotropic virus type 1 infection pathway
def: "The human T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus causing a type of cancer known as adult T-cell leukemia and lymphoma and a demyelinating condition referred to as HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). A viral regulatory protein known as Tax, which is a transcriptional co-factor, interferes with a number of signaling pathways in the host." [wikipedia:http\://en.wikipedia.org/wiki/Human_T-lymphotropic_virus]
synonym: "HTLV-1 infection pathway" EXACT []
synonym: "KEGG:05166" RELATED []
is_a: PW:0001028 ! infectious disease pathway
created_by: VPetri
creation_date: 2012-11-09T09:00:17Z

[Term]
id: PW:0001150
name: Fc receptor mediated signaling pathway
def: "Fc receptors mediated signaling exerts important regulatory and modulatory roles in immunity. Fc receptors are classified by the type of antibody they recognize. They are widely expressed on immune system cells and a number of other cell types. With one exception, they mediate activating signaling cascades." [PMID:17981207]
is_a: PW:0000235 ! adaptive immune response pathway
is_a: PW:0000820 ! signaling pathway in the adaptive immune response
created_by: VPetri
creation_date: 2012-11-09T10:50:09Z

[Term]
id: PW:0001151
name: Fc epsilon receptor mediated signaling pathway
def: "The signaling cascade initiated by an activated Fc gamma receptor. Fc receptors are classified by the type of antibody they recognize; thus, Fc epsilon receptors bind IgE antibody." [PMID:17981207]
synonym: "KEGG:04664" RELATED []
is_a: PW:0001150 ! Fc receptor mediated signaling pathway
created_by: VPetri
creation_date: 2012-11-09T11:02:34Z

[Term]
id: PW:0001152
name: steroid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of steroids. Notable examples include cholesterol and steroid hormones." [wikipedia:http\://en.wikipedia.org/wiki/Steroid]
synonym: "KEGG:00100" RELATED []
is_a: PW:0000453 ! isoprenoid biosynthetic pathway
is_a: PW:0001303 ! steroid metabolic pathway
created_by: VPetri
creation_date: 2012-11-09T15:05:33Z

[Term]
id: PW:0001153
name: caffeine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of caffeine, a xanthine alkaloid found in the seeds, leaves, and fruit of certain plants that humans use as a stimulant." [KEGG:00232, wikipedia:http\://en.wikipedia.org/wiki/Caffeine]
synonym: "KEGG:00232" RELATED []
is_a: PW:0000147 ! metabolic pathway of secondary metabolites
created_by: VPetri
creation_date: 2012-11-09T15:14:24Z

[Term]
id: PW:0001154
name: glycosaminoglycan degradation pathway
def: "Those metabolic reactions involved in the degradation of glycosaminoglycans." [KEGG:00531]
synonym: "KEGG:00531" RELATED []
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway
created_by: VPetri
creation_date: 2012-11-09T15:21:46Z

[Term]
id: PW:0001155
name: butirosin and neomycin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of butirosin and neomycin -aminoglycoside antibiotics produced by Bacillus circulans and Streptomyces fradiae, respectively." [OneLook:http\://www.onelook.com]
synonym: "KEGG:00524" RELATED []
is_a: PW:0000147 ! metabolic pathway of secondary metabolites
created_by: VPetri
creation_date: 2012-11-09T15:34:08Z

[Term]
id: PW:0001156
name: glycerolipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycerolipids which are composed of mono-, di-, and tri-substituted glycerols. Triacylglycerol, or triglyceride, is the best known example." [OneLook:http\://www.onelook.com]
synonym: "KEGG:00561" RELATED []
is_a: PW:0000010 ! lipid metabolic pathway
created_by: VPetri
creation_date: 2012-11-09T15:42:02Z

[Term]
id: PW:0001157
name: ether lipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of ether lipids. On these molecules one or more of the carbon atoms of glycerol is bonded to an alkyl group via an ether linkage." [wikipedia:http\://en.wikipedia.org/wiki/Ether_lipid]
synonym: "KEGG:00565" RELATED []
is_a: PW:0000010 ! lipid metabolic pathway
created_by: VPetri
creation_date: 2012-11-09T15:51:41Z

[Term]
id: PW:0001158
name: alpha-linoleic acid metabolic pathway
def: "Those enzymatic reactions involved in the synthesis, utilization or degradation of alpha-linoleic acid - an unsaturated omega-3 fatty acid. alpha-linoleic acid is an essential fatty acid that humans and other animals cannot synthesize and must obtain from diet." [wikipedia:http\://en.wikipedia.org/wiki/Alpha-Linolenic_acid]
synonym: "KEGG:00592" RELATED []
is_a: PW:0000058 ! fatty acid metabolic pathway
created_by: VPetri
creation_date: 2012-11-09T16:06:00Z

[Term]
id: PW:0001159
name: aminoacyl-tRNA biosynthetic pathway
def: "Aminoacyl-tRNA, or transfer RNA (tRNA) carries amino acids to ribosomes and is part of the translation pathway. tRNAs are specific for the amino acids with which they are associated. Their synthesis involves adenylation of the amino acid followed by its transfer; both steps require ATP." [wikipedia:http\://en.wikipedia.org/wiki/Aminoacyl-tRNA]
synonym: "KEGG:00970" RELATED []
relationship: part_of PW:0000101 ! translation pathway
created_by: VPetri
creation_date: 2012-11-09T16:13:47Z

[Term]
id: PW:0001160
name: RNA transport pathway
def: "The pathway thereby various RNA molecules synthesized in the nucleus are exported to the cytoplasm to be further processed such as the protein-coding mRNA or to fulfill particular functions." [PMID:15519698, PMID:21776079]
synonym: "KEGG:03013" RELATED []
synonym: "RNA nuclear export pathway" RELATED []
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
is_a: PW:0000103 ! transport pathway
created_by: VPetri
creation_date: 2012-11-12T15:25:17Z

[Term]
id: PW:0001161
name: RNA degradation pathway
def: "The turnover pathway of RNA molecules produced by the three eukaryotic polymerases. It includes the degradation of defective molecules by the RNA surveillance or decay pathway." [PMID:19239894]
synonym: "KEGG:03018" RELATED []
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
created_by: VPetri
creation_date: 2012-11-12T15:38:14Z

[Term]
id: PW:0001162
name: chemical compound signaling pathway
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2012-11-13T09:02:24Z

[Term]
id: PW:0001163
name: cannabinoid signaling pathway
def: "Cannabinoids are a class of rather diverse chemical compounds of which some, like endocannabinoids are naturally produced by the body in humans and other animals, while others are found in plants or are synthesized. Signaling is mediated by the cannabinoid receptors that are G protein coupled (GPCR) receptors. The endogenous cannabinoids are lipids and the signaling route is referred to as retrograde as it  travels 'backwards' from the postsynaptic to the presynaptic cell." [wikipedia:http\://en.wikipedia.org/wiki/Cannabinoid]
is_a: PW:0001162 ! chemical compound signaling pathway
created_by: VPetri
creation_date: 2012-11-13T09:02:41Z

[Term]
id: PW:0001164
name: endocannabinoid signaling pathway
def: "The signaling pathway initiated by the endogenous cannabinoids that activate the G protein coupled (GPCR) cannabinoid receptors and utilize a retrograde route from the postsynaptic to the presynaptic neuron." [PMID:21531987]
synonym: "KEGG:04723" RELATED []
synonym: "retrograde endocannabinoid signaling pathway" RELATED []
is_a: PW:0000959 ! lipid signaling pathway
is_a: PW:0001163 ! cannabinoid signaling pathway
created_by: VPetri
creation_date: 2012-11-13T09:19:29Z

[Term]
id: PW:0001165
name: lipid neurotransmitter metabolic pathway
is_a: PW:0000407 ! neurotransmitter metabolic pathway
created_by: VPetri
creation_date: 2012-11-13T09:46:51Z

[Term]
id: PW:0001166
name: endocannabinoid metabolic pathway
is_a: PW:0001165 ! lipid neurotransmitter metabolic pathway
created_by: VPetri
creation_date: 2012-11-13T09:47:42Z

[Term]
id: PW:0001167
name: parathyroid hormone-like hormone signaling pathway
def: "Parathyroid hormone related peptide (PTHLH) signaling exerts pleiotropic roles, unlike the related parathyroid hormone whose specific role is in calcium and phosphate homeostasis. Initially identified as a  molecule produced by certain cancers, it is now known that it is important for normal physiological functions, mostly related to development and organogenesis." [PMID:22549910]
synonym: "parathyroid hormone related peptide signaling pathway" RELATED []
synonym: "PTHrP signaling pathway" RELATED []
is_a: PW:0001180 ! parathyroid hormone family signaling pathway
created_by: VPetri
creation_date: 2013-01-04T11:32:22Z

[Term]
id: PW:0001168
name: altered calcium signaling pathway via the calcium-sensing receptor
def: "Altered calcium signaling due to mutations in the calcium-sensing receptor has been associated with a number of conditions. To date, more than 250 mutations have been identified of which more than half reside in the extracellular part of the receptor." [Casrdb:http\://www.cardb.mcgill.ca/, PMID:19484257]
is_a: PW:0001141 ! calcium signaling pathway via the calcium-sensing receptor
is_a: PW:0001169 ! altered calcium/calcium-mediated signaling pathway
created_by: VPetri
creation_date: 2013-01-04T15:17:51Z

[Term]
id: PW:0001169
name: altered calcium/calcium-mediated signaling pathway
is_a: PW:0001140 ! calcium/calcium-mediated signaling pathway
created_by: VPetri
creation_date: 2013-01-04T15:22:59Z

[Term]
id: PW:0001170
name: musculo-skeletal system drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of conditions associated with the musculo-skeletal system. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2013-01-21T15:17:57Z

[Term]
id: PW:0001171
name: tuberoinfundibular 39 residues peptide signaling pathway
def: "Tuberoinfundibular peptide of 39 residues (Tip39) is encoded by the parathyroid hormone 2 gene, weakly homologous to parathyroid hormone (PTH) and parathyroid hormone-like hormone (PTHrP). Tip39 is an endogenous ligand for the parathyroid hormone receptor 2, a G protein coupled receptor (GPCR), initially considered an orphan receptor. Signaling, mostly in the brain but also in the pancreas, testis and renal tissues, appears to involve elevation in cAMP." [PMID:19857544]
synonym: "PTH2 signaling pathway" RELATED []
synonym: "Tip39 signaling pathway" EXACT []
is_a: PW:0001180 ! parathyroid hormone family signaling pathway
created_by: VPetri
creation_date: 2013-01-28T14:00:14Z

[Term]
id: PW:0001172
name: altered fibroblast growth factor signaling pathway
def: "Fibroblast growth factor (FGF) signaling involves more than 20 proteins involved in embryonic and postnatal development and for some members, also acting as hormones in the adult. Deregulation of the pathway has been implicated in a number of neoplastic and metabolic conditions." [PMID:20940169]
synonym: "altered FGF signaling pathway" EXACT []
is_a: PW:0000298 ! altered growth factor signaling pathway
is_a: PW:0000328 ! fibroblast growth factor signaling pathway
created_by: VPetri
creation_date: 2013-01-29T09:20:46Z

[Term]
id: PW:0001173
name: intracrine fibroblast growth factor signaling pathway
def: "The fibroblast growth factors (FGF)  also known as FGF homologous factors belong to the phylogenetic subfamily FGF11/12/13/14. They signal intracellularly and independent of fibroblast growth factor receptors (FGFR). The pathway plays important neuromodulatory roles. Deregulation of the pathway has been associated with several neurodegenerative disorders." [PMID:20940169, PMID:23040813]
synonym: "intracellular FGF signaling pathway" RELATED []
synonym: "intracellular fibroblast growth factor signaling pathway" RELATED []
synonym: "intracrine FGF signaling pathway" EXACT []
is_a: PW:0000328 ! fibroblast growth factor signaling pathway
created_by: VPetri
creation_date: 2013-01-29T11:11:31Z

[Term]
id: PW:0001174
name: paracrine fibroblast growth factor signaling pathway
def: "Paracrine fibroblast growth factors (FGF) are represented by five phylogenetic subfamilies whose signaling, also referred to as canonical, is involved in the well known role of FGF in embryonic and postnatal development. Deregulation of the pathway has been associated with several conditions." [PMID:20940169]
synonym: "canonical fibroblast growth factor signaling pathway" RELATED []
synonym: "paracrine FGF signaling pathway" EXACT []
is_a: PW:0000328 ! fibroblast growth factor signaling pathway
is_a: PW:0000650 ! signaling pathway pertinent to development
created_by: VPetri
creation_date: 2013-01-29T11:20:28Z

[Term]
id: PW:0001175
name: endocrine fibroblast growth factor signaling pathway
def: "The endocrine fibroblast growth factors (FGF) also known as hormone-like belong to the 15/19/21/23 phylogenetic subfamily, also referred to as FGF19 subfamily. They have low affinity for the fibroblast growth factor receptors (FGFR) and rely on the Klotho family members to bind the receptors under physiological conditions. In particular, FGF23 signaling via Klotho, also known as the FGF23/Klotho axis plays a central role in vitamin D metabolism and renal phosphate homeostasis. Deregulation of the pathway has been associated with several conditions." [PMID:20730630, PMID:20940169, PMID:22298654]
synonym: "endocrine FGF signaling pathway" EXACT []
synonym: "fibroblast growth factor subfamily 19 signaling pathway " RELATED []
is_a: PW:0000328 ! fibroblast growth factor signaling pathway
created_by: VPetri
creation_date: 2013-01-29T11:20:53Z

[Term]
id: PW:0001176
name: altered endocrine fibroblast growth factor signaling pathway
def: "Deregulation of endocrine fibroblast growth factor signaling pathway has been associated with several paraneoplastic and metabolic diseases that include renal failure, Cushing's syndrome, type 2 diabetes and obesity, among others." [PMID:20940169]
synonym: "altered endocrine FGF signaling pathway" EXACT []
is_a: PW:0001172 ! altered fibroblast growth factor signaling pathway
is_a: PW:0001175 ! endocrine fibroblast growth factor signaling pathway
created_by: VPetri
creation_date: 2013-01-29T13:42:12Z

[Term]
id: PW:0001177
name: altered intracrine fibroblast growth factor signaling pathway
def: "Deregulation of the intracrine fibroblast growth factor signaling pathway has been associated with several neurodegenerative disorders and also with mental retardation." [PMID:20940169]
synonym: "altered intracrine FGF signaling pathway" EXACT []
is_a: PW:0001172 ! altered fibroblast growth factor signaling pathway
is_a: PW:0001173 ! intracrine fibroblast growth factor signaling pathway
created_by: VPetri
creation_date: 2013-01-29T13:47:31Z

[Term]
id: PW:0001178
name: altered paracrine fibroblast growth factor signaling pathway
def: "Deregulation of the paracrine fibroblast growth factor signaling pathway has been associated with several congenital disorders." [PMID:20940169]
synonym: "altered canonical fibroblast growth factor signaling pathway" RELATED []
synonym: "altered paracrine FGF signaling pathway" EXACT []
is_a: PW:0001172 ! altered fibroblast growth factor signaling pathway
is_a: PW:0001174 ! paracrine fibroblast growth factor signaling pathway
created_by: VPetri
creation_date: 2013-01-29T13:58:04Z

[Term]
id: PW:0001179
name: fibroblast growth factor 23 signaling pathway
def: "Fibroblast growth factor 23 signaling, a member of the endocrine subfamily of fibroblast growth factor family plays important roles in phosphate homeostasis. It is also important in vitamin D metabolism. The pathway is also referred to as the FGF23-Klotho axis, Klotho representing the obligatory co-receptor family for this subfamily with low affinity for the FGF receptors." [PMID:20059333]
synonym: "FGF23 signaling pathway" EXACT []
synonym: "FGF23/Klotho axis" RELATED []
is_a: PW:0001175 ! endocrine fibroblast growth factor signaling pathway
relationship: part_of PW:0001182 ! phosphate homeostasis pathway
created_by: VPetri
creation_date: 2013-02-04T09:00:06Z

[Term]
id: PW:0001180
name: parathyroid hormone family signaling pathway
def: "The parathyroid hormone family consists of parathyroid hormone and parathyroid hormone-like hormone that employ the same parathyroid hormone receptor type 1, a G-protein coupled receptor (GPCR) of family B of GPCRs. Despite signaling through the same receptor, the two hormones elicit distinct functions. Receptor type 2 has been considered an orphan receptor, but a specific ligand has been identified, a 39 residues peptide with weaker amino acid sequence similarity to the two hormones." [PMID:22745236]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2013-02-04T09:25:11Z

[Term]
id: PW:0001181
name: altered fibroblast growth factor 23 signaling pathway
synonym: "altered FGF23 signaling pathway" EXACT []
synonym: "altered FGF23/Klotho axis" RELATED []
is_a: PW:0001176 ! altered endocrine fibroblast growth factor signaling pathway
is_a: PW:0001179 ! fibroblast growth factor 23 signaling pathway
created_by: VPetri
creation_date: 2013-02-04T09:48:12Z

[Term]
id: PW:0001182
name: phosphate homeostasis pathway
def: "Phosphate is an essential element with many important roles in biology, from skeletal development and integrity to metabolism and cellular signaling. The greatest amount of phosphate is found in bone and teeth. The major regulator of phosphate homeostasis is  the kidney. Maintenance of proper phosphate levels is assured by an interplay of transport and signaling pathways. Sodium phosphate co-transporters, primarily type 2 and 3 and parathyroid hormone (PTH) and fibroblast growth factor 23 (FGF23) signaling are essential components." [PMID:22552885]
is_a: PW:0000355 ! homeostasis pathway
created_by: VPetri
creation_date: 2013-02-04T10:04:15Z

[Term]
id: PW:0001183
name: phosphate transport pathway
def: "The pathway that assures the proper transport of phosphate in the body Kidney plays a major role in for the filtration and reabsorption of phosphate while the bone is a principal form of storage. Several types of sodium phosphate cotransporters are involved; the role of type 2 and 3 has been established. Renal phosphate transport is under the control of parathyroid hormone (PTH) and fibroblast growth factor 23 (FGF23) signaling." [PMID:21778753]
is_a: PW:0000103 ! transport pathway
relationship: part_of PW:0001182 ! phosphate homeostasis pathway
created_by: VPetri
creation_date: 2013-02-04T10:05:08Z

[Term]
id: PW:0001184
name: altered phosphate homeostasis pathway
is_a: PW:0001182 ! phosphate homeostasis pathway
created_by: VPetri
creation_date: 2013-02-04T10:06:57Z

[Term]
id: PW:0001185
name: calcium/calmodulin dependent kinase 2 signaling pathway
def: "Calcium/calmodulin dependent kinase 2 (CAMK2) signaling plays important roles in excitation-contraction coupling in the heart and long-term potentiation (LPT) and memory in the brain." [PMID:21529938, PMID:23091085]
synonym: "CAMK2 signaling pathway" RELATED []
synonym: "CAMKII signaling pathway" EXACT []
is_a: PW:0000316 ! calcium/calmodulin dependent kinase signaling pathway
created_by: VPetri
creation_date: 2013-02-11T11:37:17Z

[Term]
id: PW:0001186
name: calcium/calmodulin dependent kinase signaling cascade
def: "The calcium/calmodulin dependent kinase signaling cascade require an upstream CAMK kinase (CAMKK) for activating phosphorylation." [PMID:21529938]
synonym: "CAMK signaling cascade" EXACT []
is_a: PW:0000316 ! calcium/calmodulin dependent kinase signaling pathway
created_by: VPetri
creation_date: 2013-02-11T11:50:56Z

[Term]
id: PW:0001187
name: calcium/calmodulin dependent kinase 1 signaling pathway
is_a: PW:0001186 ! calcium/calmodulin dependent kinase signaling cascade
created_by: VPetri
creation_date: 2013-02-11T11:55:22Z

[Term]
id: PW:0001188
name: calcium/calmodulin dependent kinase 4 signaling pathway
is_a: PW:0001186 ! calcium/calmodulin dependent kinase signaling cascade
created_by: VPetri
creation_date: 2013-02-11T11:55:57Z

[Term]
id: PW:0001189
name: altered folate metabolic pathway
def: "A folate metabolic pathway that deviates from what its normal course should be. Impairment of folate cycle and/or folate mediated one-carbon pathways is associated with an increased risk for several conditions and developmental anomalies." [PMID:15298442]
is_a: PW:0000140 ! folate metabolic pathway
is_a: PW:0000429 ! altered metabolic pathway of cofactors, vitamins, nutrients
created_by: VPetri
creation_date: 2013-03-11T11:53:52Z

[Term]
id: PW:0001190
name: altered hydrophobic amino acid metabolic pathway
is_a: PW:0000403 ! altered amino acid metabolic pathway
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
created_by: VPetri
creation_date: 2013-03-11T13:58:14Z

[Term]
id: PW:0001191
name: altered methionine cycle/metabolic pathway
def: "A methionine cycle/metabolic pathway that deviates from what its normal course should be. Impaired methionine metabolism and/or altered levels of S-adenosylmethionine (AdoMet) have been associated with hepatocellular carcinoma and alcoholic liver disease." [PMID:23073625]
is_a: PW:0000048 ! methionine cycle/metabolic pathway
is_a: PW:0001190 ! altered hydrophobic amino acid metabolic pathway
created_by: VPetri
creation_date: 2013-03-11T13:59:10Z

[Term]
id: PW:0001192
name: altered homocysteine metabolic pathway
def: "A homocysteine metabolic pathway that deviates from what its normal course should be. Enzyme and/or vitamin deficiencies or defects in folate metabolism can give rise to the abnormal levels of homocysteine in homocysteinuria or  hyperhomocystenemia and the consequences related to them." [PMID:22418620]
is_a: PW:0000398 ! homocysteine metabolic pathway
is_a: PW:0000402 ! altered metabolic pathway of other amino acids
created_by: VPetri
creation_date: 2013-03-12T10:18:13Z

[Term]
id: PW:0001193
name: kinase mediated signaling pathway
def: "Kinases are essential components of biological pathways. Phosphorylaton by protein kinases and dephosphorylation by protein phosphatases exert major regulatory roles. In addition, they can also initiate intracellular signaling cascades. Kinases represent a significant fraction of eukaryotic genes and prominent amongst them are the serine/threonine kinases." [PMID:16132230]
is_a: PW:0000003 ! signaling pathway
created_by: VPetri
creation_date: 2013-03-12T10:32:24Z

[Term]
id: PW:0001194
name: serine/threonine-specific kinase mediated signaling pathway
def: "Serine/threonine-specific kinase mediated signaling include essential intracellular pathways such as those involving the mitogen-activated (MAPK), Akt (also known as Pkb), protein kinase A and protein kinase C, to name a few. Serine/threonine-specific kinases represent the largest class." [OneLook:http\://www.onelook.com, PMID:16132230]
is_a: PW:0001193 ! kinase mediated signaling pathway
created_by: VPetri
creation_date: 2013-03-12T10:37:15Z

[Term]
id: PW:0001195
name: tyrosine-specific protein kinase mediated signaling pathway
def: "The non-receptor tyrosine-specific kinases are represented by members of Src, Jak, Syk  and other families. Some, such as Jak, function as initiators of  intracellular pathways, others are components of several pathways. Tyrosine-specific kinases are also represented by receptor tyrosine kinases activated by growth factors and hormones.  These kinases are components of the pathways the specific growth factors and hormones initiate." [PMID:16132230]
is_a: PW:0001193 ! kinase mediated signaling pathway
created_by: VPetri
creation_date: 2013-03-12T10:37:57Z

[Term]
id: PW:0001196
name: altered phosphatase mediated signaling pathway
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000652 ! phosphatase mediated signaling pathway
created_by: VPetri
creation_date: 2013-03-12T11:55:51Z

[Term]
id: PW:0001197
name: altered serine/threonine-specific phosphatase mediated signaling pathway
is_a: PW:0001196 ! altered phosphatase mediated signaling pathway
created_by: VPetri
creation_date: 2013-03-12T11:56:16Z

[Term]
id: PW:0001198
name: altered kinase mediated signaling pathway
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0001193 ! kinase mediated signaling pathway
created_by: VPetri
creation_date: 2013-03-12T12:09:21Z

[Term]
id: PW:0001199
name: altered serine/threonine-specific kinase mediated signaling pathway
is_a: PW:0001194 ! serine/threonine-specific kinase mediated signaling pathway
is_a: PW:0001198 ! altered kinase mediated signaling pathway
created_by: VPetri
creation_date: 2013-03-12T12:10:08Z

[Term]
id: PW:0001200
name: thyroid-stimulating hormone signaling pathway
def: "Thyroid-stimulating hormone (TSH) signaling stimulates the secretion of thyroid hormone. Its own secretion is dependent upon activation of thyrotropin-releasing hormone (TRH) in the hypothalamus by low levels of thyroid hormone (TH). TRH, TSH and TH signaling pathways are part of the hypothalamic-pituitary-thyroid (HPT) axis for which TH itself provides a negative regulatory loop." [PMID:22759379]
synonym: "thyrotropin signaling pathway" EXACT []
synonym: "TSH signaling pathway" EXACT []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2013-03-26T10:29:31Z

[Term]
id: PW:0001201
name: thyrotropin-releasing hormone signaling pathway
def: "Thyrotropin-releasing hormone (TRH or TRF) signaling stimulates the production of thyroid-stimulating hormone (TSH) from the pituitary, which in turn stimulates the thyroid to produce thyroid hormone (TH). TRH, TSH and TH signaling pathways are part of the hypothalamic-pituitary-thyroid (HPT) axis for which TH itself provides a negative regulatory loop." [PMID:22759379]
synonym: "thyrotropin-releasing factor signaling pathway" RELATED []
synonym: "TRF signaling pathway" RELATED []
synonym: "TRH signaling pathway" EXACT []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2013-03-26T10:47:07Z

[Term]
id: PW:0001202
name: genito-urinary system and sex hormones drug pathway
def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of genito-urinary system conditions or as sex hormones derivatives and analogs. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2013-03-26T11:29:09Z

[Term]
id: PW:0001203
name: systemic hormones drug pathway
def: "The pharmacokinetics and pharmacodynamics of hormonal preparations that may contain natural hormones or are synthetic hormonal analogs and their derivatives.  It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [KEGG:http\://www.genome.jp/kegg-bin/get_htext?br08303.keg]
is_a: PW:0000754 ! drug pathway
created_by: VPetri
creation_date: 2013-03-26T12:01:13Z

[Term]
id: PW:0001204
name: thyromimetics drug pathway
def: "The pharmacokinetics and pharmacodynamics of thyroid hormone analogs, many of which have tissue specific thyroid hormone action." [PMID:21504761]
is_a: PW:0001203 ! systemic hormones drug pathway
created_by: VPetri
creation_date: 2013-03-26T12:24:40Z

[Term]
id: PW:0001205
name: sobetirome drug pathway
def: "Sobetirome, also known as GC-1, is a one of the best characterized thyromimetics with high affinity for the beta thyroid receptor. It has been shown to reduce LDL cholesterol in animal model studies." [PMID:21504761]
is_a: PW:0001204 ! thyromimetics drug pathway
created_by: VPetri
creation_date: 2013-03-26T12:31:54Z

[Term]
id: PW:0001206
name: eprotirome drug pathway
def: "Eprotirome is a thyromimetics that in addition for being selective for the beta tyrosine receptor is also highly liver-selective with minimal uptake in non-hepatic tissues. In overweight and hypercholesterolemic patients, its administration lead to lowering of total and LDL-cholesterol while stimulating bile acid biosynthesis." [PMID:21504761]
is_a: PW:0001204 ! thyromimetics drug pathway
created_by: VPetri
creation_date: 2013-03-26T12:36:58Z

[Term]
id: PW:0001207
name: folate cycle metabolic pathway
def: "The folate cycle metabolic pathway sums up the uptake and transport of folates, the processing and interconversion reactions of folate compounds. The folate cycle and the folate mediate one-carbon transfer pathways are part of folate metabolism." [PMID:11001804, PMID:15166809, PMID:15298442]
relationship: part_of PW:0000140 ! folate metabolic pathway
created_by: VPetri
creation_date: 2013-04-02T09:58:52Z

[Term]
id: PW:0001208
name: altered folate cycle metabolic pathway
is_a: PW:0001189 ! altered folate metabolic pathway
is_a: PW:0001207 ! folate cycle metabolic pathway
created_by: VPetri
creation_date: 2013-04-02T10:06:47Z

[Term]
id: PW:0001209
name: altered folate mediated one-carbon metabolic pathway
is_a: PW:0000189 ! folate mediated one-carbon metabolic pathway
is_a: PW:0001189 ! altered folate metabolic pathway
created_by: VPetri
creation_date: 2013-04-02T10:07:30Z

[Term]
id: PW:0001210
name: plevitrexed drug pathway
def: "The pharmacokinetics and pharmacodynamics of plevitrexed, a non-polyglutamatable antifolate quinazoline derivative and thymidylate synthase inhibitor used in the treatment of cancers. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [NCI:http\://www.cancer.gov]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:15:35Z

[Term]
id: PW:0001211
name: plevitrexed pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of plevitrexed, an antifolate used in the treatment of cancer. Genetic variations can result in changes in the availability of the drug." [NCI:NCI, wikipedia:www.cancer.gov]
is_a: PW:0001210 ! plevitrexed drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:18:45Z

[Term]
id: PW:0001212
name: plevitrexed pharmacodynamics pathway
def: "The pathway of plevitrexed-target interactions and of the biochemical or physiological responses to drug. The drug is an antifolate that targets thymidylate synthase and is used in the treatment of several cancers. Genetic variations can cause differences in the response of the organism to the drug." [NCI:NCI, wikipedia:www.cancer.gov]
is_a: PW:0001210 ! plevitrexed drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:19:15Z

[Term]
id: PW:0001213
name: pemetrexed drug pathway
def: "The pharmacokinetics and pharmacodynamics of permetrexed, an antifolate originally designed as a thymidylate synthase inhibitor but which also has inhibitory effects on other enzymes involved in the folate cycle and/or folate mediated one-carbon transfer reactions. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [Wikipedia:http\://en.wikipedia.org/wiki/Pemetrexed]
synonym: "Alimta drug pathway" RELATED []
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:21:07Z

[Term]
id: PW:0001214
name: pemetrexed pharmacodynamics pathway
def: "The pathway of pemetrexed-target interactions and of the biochemical or physiological responses to drug. The drug is an antifolate that targets thymidylate synthase and other enzymes of the folate cycle and folate mediated one-carbon transfer reactions and is used in the treatment of several cancers. Genetic variations can cause differences in the response of the organism to the drug." [NCI; wikipedia:www.cancer.gov]
synonym: "Alimta pharmacodynamics pathway" RELATED []
is_a: PW:0001213 ! pemetrexed drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:27:10Z

[Term]
id: PW:0001215
name: pemetrexed pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of pemetrexed, an antifolate used in the treatment of cancer. Genetic variations can result in changes in the availability of the drug." [NCI; wikipedia:www.cancer.gov]
synonym: "Alimta pharmacokinetics pathway" RELATED []
is_a: PW:0001213 ! pemetrexed drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:27:34Z

[Term]
id: PW:0001216
name: pralatrexate drug pathway
def: "The pharmacokinetics and pharmacodynamics of pralatrexate, a polyglutamatable antifolate used as an inhibitor of dihydrofolate reductase (DHFR) enzyme of folate cycle. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [Wikipedia:http\://en.wikipedia.org/wiki/Pralatrexate]
synonym: "Folotyn drug pathway" RELATED []
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:34:53Z

[Term]
id: PW:0001217
name: pralatrexate pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of pralatrexed, an antifolate used in the treatment of cancer. Genetic variations can result in changes in the availability of the drug." [NCI\\; wikipedia:www.cancer.gov]
synonym: "Folotyn pharmacokinetics pathway" RELATED []
is_a: PW:0001216 ! pralatrexate drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:38:36Z

[Term]
id: PW:0001218
name: pralatrexate pharmacodynamics pathway
def: "The pathway of pralatrexed-target interactions and of the biochemical or physiological responses to drug. The drug is an antifolate that targets dihydrofolate reductase (DHFR) and is used in the treatment of some cancers. Genetic variations can cause differences in the response of the organism to the drug." [NCI; wikipedia:www.cancer.gov]
synonym: "Folotyn pharmacodynamics pathway" RELATED []
is_a: PW:0001216 ! pralatrexate drug pathway
created_by: VPetri
creation_date: 2013-04-05T09:39:53Z

[Term]
id: PW:0001219
name: hydrogen sulfide mediated signaling pathway
def: "Hydrogen sulfide can act as a signaling molecule with roles in the heart, brain and smooth muscle." [PMID:20067586, PMID:22546339, PMID:22781905]
synonym: "H2S signaling pathway" RELATED []
is_a: PW:0001221 ! gasotransmitter mediated signaling pathway
created_by: VPetri
creation_date: 2013-04-16T11:11:57Z

[Term]
id: PW:0001220
name: nitric oxide mediated signaling pathway
synonym: "NO mediated signaling pathway" RELATED []
is_a: PW:0001221 ! gasotransmitter mediated signaling pathway
created_by: VPetri
creation_date: 2013-04-16T11:14:49Z

[Term]
id: PW:0001221
name: gasotransmitter mediated signaling pathway
def: "Those signaling pathway elicited by gases such as carbon monoxide, nitric oxide or hydrogen sulfide." [PMID:22546339, PMID:22781905]
is_a: PW:0001162 ! chemical compound signaling pathway
created_by: VPetri
creation_date: 2013-04-16T11:20:16Z

[Term]
id: PW:0001222
name: forkhead class C signaling pathway
synonym: "FoxC signaling pathway" RELATED []
is_a: PW:0000647 ! forkhead signaling pathway
created_by: VPetri
creation_date: 2013-05-02T09:37:31Z

[Term]
id: PW:0001223
name: forkhead class P signaling pathway
synonym: "FoxP signaling pathway" RELATED []
is_a: PW:0000647 ! forkhead signaling pathway
created_by: VPetri
creation_date: 2013-05-02T09:38:33Z

[Term]
id: PW:0001224
name: irinotecan drug pathway
def: "The pharmacokinetics and pharmacodynamics of irinotecan an inhibitor of DNA topoisomerase I used in the treatment of several types of cancer. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2013-05-03T10:54:39Z

[Term]
id: PW:0001225
name: irinotecan pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of irinotecan, a drug used in the treatment of several types of cancer. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA2001]
is_a: PW:0001224 ! irinotecan drug pathway
created_by: VPetri
creation_date: 2013-05-03T10:58:59Z

[Term]
id: PW:0001226
name: irinotecan pharmacodynamics pathway
def: "The pathway of irinotecan-target interactions and of the biochemical or physiological responses to drug. Irinotecan is a DNA topoisomerase I inhibitor used in the treatment of several types of cancer. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA2029]
is_a: PW:0001224 ! irinotecan drug pathway
created_by: VPetri
creation_date: 2013-05-03T10:59:18Z

[Term]
id: PW:0001227
name: Stem Cell Factor signaling pathway
def: "The Stem Cell Factor (SCF) signaling plays important roles in cell migration, proliferation and survival. SCF activates the KIT receptor tyrosine kinase which then prompts several intracellular signaling pathways. Deregulation of the pathway has been associated with several conditions including cancer." [PMID:23073628]
synonym: "SCF signaling pathway" EXACT []
synonym: "Steel factor signaling pathway" EXACT []
is_a: PW:0000168 ! growth factor signaling pathway
created_by: VPetri
creation_date: 2013-05-03T11:24:34Z

[Term]
id: PW:0001228
name: ACE inhibitor drug pathway
def: "The pharmacokinetics and pharmacodynamics of drugs that target the angiotensin converting enzyme ACE. In the renin-angiotensin cascade,  several bioactive peptides are derived from the precursor angiotensinogen. ACE converts angiotensin I to the potent angiotensin II. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [WHO:http\://www.whocc.no/atc_ddd_index]
is_a: PW:0000920 ! cardiovascular system drug pathway
created_by: VPetri
creation_date: 2013-05-03T11:54:00Z

[Term]
id: PW:0001229
name: xenobiotic metabolic pathway
def: "Those metabolic reactions involved in the uptake, modification and elimination of chemical compounds that are foreign to the biological system. This includes the biotransformation pathways organisms use to detoxify the system and the degradation of toxic pollutants by microorganisms. Many of the compounds that enter the cell are inactive and the transformation pathways aim to increase their hydrophilicity and ease the elimination.  In the process, some of the intermediates may give rise to toxic metabolites and effects. The transformation pathways are also important for the pharmacokinetics aspect of drug metabolism.  The distinction is that a drug is a foreign compound intentionally administered. In the case of the degradation pathway, microoganismal  enzymes have the ability to degrade otherwise resistant compounds." []
is_a: PW:0000002 ! classic metabolic pathway
created_by: VPetri
creation_date: 2013-05-03T15:29:08Z

[Term]
id: PW:0001230
name: ACE inhibitor pharmacokinetics pathway
is_a: PW:0001228 ! ACE inhibitor drug pathway
created_by: VPetri
creation_date: 2013-05-07T16:04:48Z

[Term]
id: PW:0001231
name: ACE inhibitor pharmacodynamics pathway
is_a: PW:0001228 ! ACE inhibitor drug pathway
created_by: VPetri
creation_date: 2013-05-07T16:05:08Z

[Term]
id: PW:0001232
name: arylamine metabolic pathway
is_a: PW:0001229 ! xenobiotic metabolic pathway
created_by: VPetri
creation_date: 2013-05-07T16:22:19Z

[Term]
id: PW:0001233
name: benzo(a)pyrene metabolic pathway
def: "Those metabolic reaction involved in handling this polycyclic aromatic hydrocarbon whose metabolites are mutagenic and carcinogenic." [Wikipedia:http\://en.wikipedia.org/wiki/Benzo%28a%29pyrene]
is_a: PW:0001438 ! polycyclic aromatic hydrocarbon metabolic pathway
created_by: VPetri
creation_date: 2013-05-07T16:24:12Z

[Term]
id: PW:0001234
name: biogenic amine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of biogenic amines." [PMID:12641342]
is_a: PW:0000211 ! biogenic amines and polyamines metabolic pathway
created_by: VPetri
creation_date: 2013-05-08T08:31:26Z

[Term]
id: PW:0001235
name: catecholamine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of catecholamines. Epinephrine, norepinephrine and dopamine are among the most abundant and are produced primarily from the adrenal medulla and the postganglionic fibers of the sympathetic nervous system." [PMID:19342614]
is_a: PW:0000443 ! catecholamine metabolic pathway
is_a: PW:0001234 ! biogenic amine biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T08:33:31Z

[Term]
id: PW:0001236
name: histamine biosynthetic pathway
is_a: PW:0000411 ! histamine metabolic pathway
is_a: PW:0001238 ! indoleamine and related compounds biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T08:38:25Z

[Term]
id: PW:0001237
name: serotonin biosynthetic pathway
is_a: PW:0000410 ! serotonin metabolic pathway
is_a: PW:0001238 ! indoleamine and related compounds biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T08:38:42Z

[Term]
id: PW:0001238
name: indoleamine and related compounds biosynthetic pathway
is_a: PW:0000444 ! indoleamine and related compounds metabolic pathway
is_a: PW:0001234 ! biogenic amine biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T08:39:39Z

[Term]
id: PW:0001239
name: eicosanoid biosynthetic pathway
def: "Those metabolic reaction involved in the synthesis of eicosanoids, molecules that play important roles in the immune and vascular systems. They are derived from either omega-3 or omega-6 fatty acids, with the route provided by the conversion of arachidonic acid, better known." [PMID:15896353]
is_a: PW:0000485 ! eicosanoid metabolic pathway
created_by: VPetri
creation_date: 2013-05-08T09:54:38Z

[Term]
id: PW:0001240
name: prostanoid metabolic pathway
def: "Prostanoids are a class of eicosanoids that contains the prostaglandins, the thromboxanes and the prostacyclines." [PMID:15896353]
is_a: PW:0000485 ! eicosanoid metabolic pathway
created_by: VPetri
creation_date: 2013-05-08T10:04:12Z

[Term]
id: PW:0001241
name: prostacyclin metabolic pathway
def: "Those metabolic reactions involving prostacyclines - a family of prostanoid eicosanoids with many regulatory functions." [PMID:15896353]
is_a: PW:0001240 ! prostanoid metabolic pathway
created_by: VPetri
creation_date: 2013-05-08T10:09:06Z

[Term]
id: PW:0001242
name: leukotriene biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of leukotriene, a class of eicosanoids, molecules exerting important roles in the immune and vascular systems." [PMID:15896353]
is_a: PW:0000464 ! leukotriene metabolic pathway
is_a: PW:0001239 ! eicosanoid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T10:16:22Z

[Term]
id: PW:0001243
name: prostanoid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of prostanoids, a class of eicosanoids including several families and exerting important roles in the immune and vascular systems." [PMID:15896353]
is_a: PW:0001239 ! eicosanoid biosynthetic pathway
is_a: PW:0001240 ! prostanoid metabolic pathway
created_by: VPetri
creation_date: 2013-05-08T10:18:59Z

[Term]
id: PW:0001244
name: codeine and morphine drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of codeine and morphine, a class of drugs in the opiate family used as pain relievers. Both are naturally found in the poppy plant with codeine synthesized from the more abundant morphine. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA146123006]
is_a: PW:0000923 ! nervous system drug pathway
created_by: VPetri
creation_date: 2013-05-08T10:38:09Z

[Term]
id: PW:0001245
name: codeine and morphine pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of codeine and morphine, a class of drug opiates used as pain relievers. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA146123006]
is_a: PW:0001244 ! codeine and morphine drug pathway
created_by: VPetri
creation_date: 2013-05-08T10:42:00Z

[Term]
id: PW:0001246
name: codeine and morphine pharmacodynamics pathway
def: "The pathway of codeine/morphine-target interaction and of the biochemical or physiological responses to drug. The drugs are potential ligands for the mu-opioid receptor, a class of opioid receptor. Opioid receptors are G-protein coupled receptors (GPCR) activated by endogenous and also exogenous opioids. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA146123006]
is_a: PW:0001244 ! codeine and morphine drug pathway
created_by: VPetri
creation_date: 2013-05-08T10:42:23Z

[Term]
id: PW:0001247
name: nifedipine drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of nifedipine, a calcium channel blocker used primarily in the treatment of hypertension and angina. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:18793108]
synonym: "Adalat CC drug pathway" RELATED []
synonym: "Procardia drug pathway" RELATED []
is_a: PW:0000920 ! cardiovascular system drug pathway
created_by: VPetri
creation_date: 2013-05-08T11:07:26Z

[Term]
id: PW:0001248
name: nifedipine pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of nifedipine. The drug is a calcium channel blocker used in the treatment of hypertension and angina.  Genetic variations can result in changes in the availability of the drug." [Wikipedia:http\://en.wikipedia.org/wiki/Nifedipine]
is_a: PW:0001247 ! nifedipine drug pathway
created_by: VPetri
creation_date: 2013-05-08T11:17:54Z

[Term]
id: PW:0001249
name: nifedipine pharmacodynamics pathway
def: "The pathway of nifedipine-target interaction and of the biochemical or physiological responses to them. The drug is a calcium channel blocker, particularly the L-type channel.  Genetic variations can cause differences in the response of the organism to the drug." [PMID:17307972]
is_a: PW:0001247 ! nifedipine drug pathway
created_by: VPetri
creation_date: 2013-05-08T11:18:25Z

[Term]
id: PW:0001250
name: monoamine transport pathway
def: "The pathway responsible for the transport of monoamines, biogenic amines representing various neurotransmitters. The reuptake of neurotransmitters following their release is a key element determining the duration and intensity of their signaling and is thus essential for the proper functioning of the nervous system." [PMID:12511858, PMID:16024510]
synonym: "biogenic amine neurotransmitter transport pathway" RELATED []
is_a: PW:0000103 ! transport pathway
is_a: PW:0001251 ! regulatory pathway pertinent to the brain
created_by: VPetri
creation_date: 2013-05-08T11:50:06Z

[Term]
id: PW:0001251
name: regulatory pathway pertinent to the brain
is_a: PW:0000004 ! regulatory pathway
created_by: VPetri
creation_date: 2013-05-08T12:07:10Z

[Term]
id: PW:0001252
name: prolactin signaling pathway
def: "Prolactin signaling pathway is important for normal reproduction. Prolactin is a peptide hormone whose signaling activates several intracellular cascades." [PMID:21664429, PMID:22684822]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
created_by: VPetri
creation_date: 2013-05-08T12:14:48Z

[Term]
id: PW:0001253
name: fatty acid omega degradation pathway
def: "The omega degradation pathway is an alternative route to the common beta degradation pathway." [PMID:21156023]
synonym: "fatty acid omega oxidation pathway" RELATED []
is_a: PW:0000642 ! fatty acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T12:38:21Z

[Term]
id: PW:0001254
name: amino acid biosynthetic pathway
is_a: PW:0000011 ! amino acid metabolic pathway
created_by: VPetri
creation_date: 2013-05-08T12:55:19Z

[Term]
id: PW:0001255
name: hydrophilic amino acid biosynthetic pathway
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
is_a: PW:0001254 ! amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T12:55:35Z

[Term]
id: PW:0001256
name: hydrophobic amino acid biosynthetic pathway
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
is_a: PW:0001254 ! amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T12:55:59Z

[Term]
id: PW:0001257
name: amino acid degradation pathway
is_a: PW:0000011 ! amino acid metabolic pathway
created_by: VPetri
creation_date: 2013-05-08T12:56:23Z

[Term]
id: PW:0001258
name: hydrophobic amino acid degradation pathway
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
is_a: PW:0001257 ! amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T12:56:41Z

[Term]
id: PW:0001259
name: hydrophilic amino acid degradation pathway
is_a: PW:0001075 ! hydrophilic amino acid metabolic pathway
is_a: PW:0001257 ! amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T12:57:01Z

[Term]
id: PW:0001260
name: arginine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of arginine. Although primarily a non-essential amino acid, its synthesis from citrulline may be insufficient and it is also energetically costly. Diet derived arginine can circumvent these aspects." [Wikipedia:http\://en.wikipedia.org/wiki/Arginine]
is_a: PW:0001082 ! arginine metabolic pathway
is_a: PW:0001255 ! hydrophilic amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T13:06:34Z

[Term]
id: PW:0001261
name: arginine degradation pathway
def: "Those metabolic reactions involved in the degradation of arginine. Higher organisms do not possess the enzymes involved in this catabolic pathway." [MetaCyc:http\://www.biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=AST-PWY]
is_a: PW:0001082 ! arginine metabolic pathway
is_a: PW:0001259 ! hydrophilic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T13:21:38Z

[Term]
id: PW:0001262
name: glutamic acid/glutamate biosynthetic pathway
def: "Those metabolic reaction involved in the biosynthesis of glutamic acid/glutamate. Glutamate is the main excitatory neurotransmitter." []
is_a: PW:0000027 ! glutamic acid/glutamate metabolic pathway
is_a: PW:0001255 ! hydrophilic amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T13:30:08Z

[Term]
id: PW:0001263
name: glutamic acid/glutamate degradation pathway
def: "Those metabolic reactions involved in the degradation of glutamic acid/glutamate. There are several routes of glutamic acid/glutamate degradation. Some are found only in microorganisms and plants; others can be found in mammalian cells." []
is_a: PW:0000027 ! glutamic acid/glutamate metabolic pathway
is_a: PW:0001259 ! hydrophilic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T13:46:32Z

[Term]
id: PW:0001264
name: glycine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of glycine, a major inhibitory neurotransmitter." [Wikipedia:http\://en.wikipedia.org/wiki/Glycine]
is_a: PW:0000440 ! glycine metabolic pathway
is_a: PW:0001256 ! hydrophobic amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T13:51:53Z

[Term]
id: PW:0001265
name: glycine degradation pathway
def: "Those metabolic reactions involved in the degradation of glycine. Several routes are available of which the glycine cleavage system is the predominant one. It occurs in the mitochondria and produces 5,10-methylene tetrahydrofolate and as such, is an important component of folate cycle pathway." [PMID:18941301, wikipedia:http\://en.wikipedia.org/wiki/Glycine]
is_a: PW:0000440 ! glycine metabolic pathway
is_a: PW:0001258 ! hydrophobic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T13:54:02Z

[Term]
id: PW:0001266
name: histidine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of histidine, an essential amino acid for humans. The biosynthesis of histidine has been extensively studied in E. coli and S. typhimurium." [PMID:8852895]
is_a: PW:0000051 ! histidine metabolic pathway
is_a: PW:0001255 ! hydrophilic amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T14:06:42Z

[Term]
id: PW:0001267
name: histidine degradation pathway
def: "Those metabolic reactions involved in the degradation of histidine." []
is_a: PW:0000051 ! histidine metabolic pathway
is_a: PW:0001259 ! hydrophilic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T14:13:58Z

[Term]
id: PW:0001268
name: isoleucine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of isoleucine, an essential amino acid for humans. Its synthesis in plants and microorganisms proceeds via several steps." [wikipedia:http\://en.wikipedia.org/wiki/Isoleucine]
is_a: PW:0001087 ! isoleucine metabolic pathway
is_a: PW:0001256 ! hydrophobic amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T14:24:37Z

[Term]
id: PW:0001269
name: isoleucine degradation pathway
def: "Those metabolic reactions involved in the degradation of isoleucine." []
is_a: PW:0001087 ! isoleucine metabolic pathway
is_a: PW:0001258 ! hydrophobic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T14:37:44Z

[Term]
id: PW:0001270
name: leucine biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of leucine, an essential amino acid for humans. In plants and microorganisms its synthesis proceeds via a number of steps." [Wikipedia:http\://en.wikipedia.org/wiki/Leucine]
is_a: PW:0001088 ! leucine metabolic pathway
is_a: PW:0001256 ! hydrophobic amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-08T14:40:17Z

[Term]
id: PW:0001271
name: leucine degradation pathway
def: "Those metabolic reactions involved in the degradation of leucine." [Wikipedia:http\://en.wikipedia.org/wiki/Leucine]
is_a: PW:0001088 ! leucine metabolic pathway
is_a: PW:0001258 ! hydrophobic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-08T14:44:17Z

[Term]
id: PW:0001272
name: RNA polymerase transcription pathway
def: "The pathway of DNA transcription carried out by the prokaryotic and several eukaryotic polymerases." []
is_a: PW:0000100 ! transcription pathway
created_by: VPetri
creation_date: 2013-05-13T08:54:54Z

[Term]
id: PW:0001273
name: prokaryotic RNA polymerase transcription pathway
def: "The pathway of DNA transcription in prokaryotic organisms is carried out by a single polymerase. Five subunits constitute the core enzyme." [OneLook:http\://www.onelook.com]
is_a: PW:0001272 ! RNA polymerase transcription pathway
created_by: VPetri
creation_date: 2013-05-13T08:58:26Z

[Term]
id: PW:0001274
name: RNA polymerase II transcription initiation pathway
def: "RNA polymerase II and a set of general and specific transcription factors assemble as a large pre-initiation complex which undergoes a series of transformations before transcription proceeds. Promoter recognition and subsequent initiation of transcription are dependent upon the presence of these transcription factors. Activators and repressors impact upon transcription at these early stages." [PMID:23000482]
relationship: part_of PW:0000127 ! RNA polymerase II transcription pathway
created_by: VPetri
creation_date: 2013-05-13T09:10:45Z

[Term]
id: PW:0001275
name: eukaryotic RNA polymerase transcription pathway
def: "The pathway of DNA transcription carried out by several eukaryotic polymerases." []
is_a: PW:0001272 ! RNA polymerase transcription pathway
created_by: VPetri
creation_date: 2013-05-13T09:13:57Z

[Term]
id: PW:0001276
name: de novo nicotinamide adenine dinucleotide biosynthetic pathway
def: "Those metabolic reactions involved in the de novo synthesis of nicotinamide adenine dinucleotide (NAD) from tryptophan." [PMID:18429699]
is_a: PW:0000219 ! nicotinamide adenine dinucleotide biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-13T09:35:26Z

[Term]
id: PW:0001277
name: glutathione biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of glutathione. Glutathione is a tripeptide that exerts important functions as an antioxidant and in the conjugation of xenobiotics and drugs by phase II biotransformation enzymes." [PMID:22998389, PMID:23201762]
is_a: PW:0000134 ! glutathione metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T09:49:41Z

[Term]
id: PW:0001278
name: threonine biosynthetic pathway
def: "Those metabolic reaction involved in the synthesis of threonine. Threonine is an essential amino acid that human cannot synthesize. Its synthesis takes place in plants and microorganisms." [wikipedia:http\://en.wikipedia.org/wiki/Threonine]
is_a: PW:0001085 ! threonine metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T10:35:40Z

[Term]
id: PW:0001279
name: threonine degradation pathway
def: "Those metabolic reactions involved in the degradation of threonine, an essential amino acid for humans. There are several routes for the degradation of  threonine." []
is_a: PW:0001085 ! threonine metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T10:48:43Z

[Term]
id: PW:0001280
name: tryptophan biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of tryptophan, an essential amino acid that human cannot synthesize. Its synthesis takes place in plants and microorganisms. In plants, the synthesis of aromatic amino acids is part of chorismate pathway, the end branch point of shikimate pathway." [PMID:20817774, wiki[pedia:http\://en.wikipedia.org/wiki/Tryptophan]
is_a: PW:0000054 ! tryptophan metabolic pathway
is_a: PW:0001256 ! hydrophobic amino acid biosynthetic pathway
relationship: part_of PW:0001370 ! chorismate metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T11:10:00Z

[Term]
id: PW:0001281
name: tryptophan degradation pathway
def: "Those metabolic reactions involved in the degradation of tryptophan, an essential amino acid.  Tryptophan undergoes oxidative catabolism carried out by several hemeprotein enzymes. In plants, tyrosine is the precursor for several secondary metabolites." [PMID:20817774, PMID:22889220]
is_a: PW:0000054 ! tryptophan metabolic pathway
is_a: PW:0001258 ! hydrophobic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-13T11:18:16Z

[Term]
id: PW:0001282
name: kynurenine metabolic pathway
def: "Those metabolic reactions involved in the production of kynurenine, a product of tryptophan degradation pathway. Kynurenine and its metabolites play important roles in the nervous system and also in immunity." [PMID:21744051, PMID:22139324]
is_a: PW:0001281 ! tryptophan degradation pathway
created_by: VPetri
creation_date: 2013-05-13T11:34:39Z

[Term]
id: PW:0001283
name: tyrosine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of tyrosine. In mammals, is derived from phenylalanine or from diet. In plants, is produced as part of chorismate pathway, the end branch point of shikimate pathway." [PMID:20817774, wikipedia:http\://en.wikipedia.org/wiki/Tyrosine]
is_a: PW:0000052 ! tyrosine metabolic pathway
is_a: PW:0001256 ! hydrophobic amino acid biosynthetic pathway
relationship: part_of PW:0001370 ! chorismate metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T11:48:30Z

[Term]
id: PW:0001284
name: tyrosine degradation pathway
def: "Those metabolic reactions involved in the degradation and/or conversion of tyrosine, an essential amino acid for humans. Tyrosine is the precursor of several neurotransmitters and hormones. Tyrosine can also be degraded to acetoacetate and fumarate. In plants, tyrosine is the precursor of several families of secondary metabolites." [PMID:20817774]
is_a: PW:0000052 ! tyrosine metabolic pathway
is_a: PW:0001258 ! hydrophobic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-13T12:01:22Z

[Term]
id: PW:0001285
name: valine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of valine, an essential amino acid for humans. Plants synthesize valine from pyruvic acid via a number of steps." [wikipedia:http\://en.wikipedia.org/wiki/Valine]
is_a: PW:0001080 ! valine metabolic pathway
is_a: PW:0001256 ! hydrophobic amino acid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-13T12:36:05Z

[Term]
id: PW:0001286
name: valine degradation pathway
is_a: PW:0001080 ! valine metabolic pathway
is_a: PW:0001258 ! hydrophobic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-13T12:40:08Z

[Term]
id: PW:0001287
name: phenylalanine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of phenylalanine, an essential amino acid for humans. In plants, the synthesis of aromatic amino acids is part of chorismate pathway, the end branch point of shikimate pathway." [PMID:20817774]
is_a: PW:0000053 ! phenylalanine metabolic pathway
is_a: PW:0001256 ! hydrophobic amino acid biosynthetic pathway
relationship: part_of PW:0001370 ! chorismate metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T12:42:31Z

[Term]
id: PW:0001288
name: phenylalanine degradation pathway
def: "Those metabolic reactions involved in the degradation and/or conversion of phenylalanine. Phenylalanine is the precursor of tyrosine, in turn a precursor for a number of neurotransmitters and hormones. In plants, phenylalanine serve as a precursor for a large number of functional secondary metabolites." [PMID:20817774]
is_a: PW:0000053 ! phenylalanine metabolic pathway
is_a: PW:0001258 ! hydrophobic amino acid degradation pathway
created_by: VPetri
creation_date: 2013-05-13T12:42:59Z

[Term]
id: PW:0001289
name: carotene metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of carotene collectively referring to several related unsaturated hydrocarbon compounds that are synthesized by plants. Some are vitamin precursors, such as the beta-carotene precursor of vitamin A." [wikipedia:https\://en.wikipedia.org/wiki/Carotene]
is_a: PW:0000005 ! carbohydrate metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T12:52:07Z

[Term]
id: PW:0001290
name: lycopene metabolic pathway
def: "Those metabolic reactions involved ion the synthesis, utilization and/or degradation of lycopene - a carotene and phytochemical found in red fruits and vegetables." [wikipedia:https\://en.wikipedia.org/wiki/Lycopene]
is_a: PW:0001289 ! carotene metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T13:00:59Z

[Term]
id: PW:0001291
name: lycopene biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of lycopene, a carotene and phytochemical found in red fruits and vegetables. Plants and bacteria have the ability to synthesize lycopene." [MetaCyc:http\://biocyc.org/META/NEW-IMAGE?object=Lycopene-Biosynthesis]
is_a: PW:0001290 ! lycopene metabolic pathway
is_a: PW:0001292 ! carotene biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-13T13:03:31Z

[Term]
id: PW:0001292
name: carotene biosynthetic pathway
is_a: PW:0001289 ! carotene metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T13:07:34Z

[Term]
id: PW:0001293
name: carotene degradation pathway
is_a: PW:0001289 ! carotene metabolic pathway
created_by: VPetri
creation_date: 2013-05-13T13:07:52Z

[Term]
id: PW:0001294
name: eicosanoid signaling pathway
def: "Eicosanoids, derived from omega-3 or omega-6 fatty acids, are represented by the leukotriene and prostanoid classes of which the latter is represented by several families. Some can act as endogenous ligands for members of the peroxisomal proliferator-activated nuclear receptors (PPARs). Once activated, PPARs heterodimerize with the retinoid X receptor (RXR) and modulate the expression of target genes." [PMID:17132851]
is_a: PW:0000959 ! lipid signaling pathway
created_by: VPetri
creation_date: 2013-05-13T13:46:40Z

[Term]
id: PW:0001295
name: leukotriene signaling pathway
def: "Leukotriene are eicosanoids derived from omega-3 or omega-6 fatty acids. Some can act as natural agonists of peroxisomal proliferator-activated nuclear receptors (PPARs)." [PMID:17132851]
is_a: PW:0001294 ! eicosanoid signaling pathway
created_by: VPetri
creation_date: 2013-05-14T11:35:27Z

[Term]
id: PW:0001296
name: prostanoid signaling pathway
def: "Prostanoids are eicosanoids derived from omega-3 or omega-6 fatty acids and represented by several families. Some can act as natural agonists of peroxisomal proliferator-activated nuclear receptors (PPARs)." [PMID:17132851]
is_a: PW:0001294 ! eicosanoid signaling pathway
created_by: VPetri
creation_date: 2013-05-14T12:36:29Z

[Term]
id: PW:0001297
name: prostaglandin signaling pathway
def: "Prostaglandins are one of several families of prostanoids, eicosanoids derived from omega-3 or omega-6 fatty acids. Some can act as natural agonists of peroxisomal proliferator-activated nuclear receptors (PPARs)." [PMID:17132851]
is_a: PW:0001296 ! prostanoid signaling pathway
created_by: VPetri
creation_date: 2013-05-14T12:40:57Z

[Term]
id: PW:0001298
name: trehalose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of trehalose - a disaccharide synthesized by bacteria, fungi, plants and invertebrates. It has important roles in plant development and it represents the energy storage that insects use for flight. It is believed to be involved in the ability of plants and animals to withstand long periods of desiccation or anhydrobiosis." [PMID:22140246]
synonym: "mycose metabolic pathway" RELATED []
synonym: "tremalose metabolic pathway" RELATED []
is_a: PW:0000005 ! carbohydrate metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T12:52:29Z

[Term]
id: PW:0001299
name: trehalose biosynthetic pathway
def: "Those metabolic reactions involved on the synthesis of trehalose, a disaccharide found in bacteria, fungi, plants and invertebrates." [PMID:22140246]
synonym: "mycose biosynthetic pathway" RELATED []
synonym: "tremalose biosynthetic pathway" RELATED []
is_a: PW:0001298 ! trehalose metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T13:14:46Z

[Term]
id: PW:0001300
name: trehalose degradation pathway
def: "Those metabolic reactions involved in the degradation of trehalose. While the synthesis of trehalose does not take place in vertebrates, the catabolic route of its metabolism does occur." [SMPDB:http\://pathman.smpdb.ca/pathways/SMP00467/pathway]
synonym: "mycose degradation pathway" RELATED []
synonym: "tremalose degradation pathway" RELATED []
is_a: PW:0001298 ! trehalose metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T13:20:57Z

[Term]
id: PW:0001301
name: methionine biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of methionine. As an essential amino acid, methionine can not be synthesized by humans. Its synthesis takes place in plants and microorganisms." [wikipedia:http\://en.wikipedia.org/wiki/Methionine]
is_a: PW:0000048 ! methionine cycle/metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T13:45:19Z

[Term]
id: PW:0001302
name: methionine degradation pathway
def: "Those metabolic reactions involved in the degradation of methionine. In higher organisms methionine is either recycled via the remethylation pathways or is converted to cysteine via the transsulfuration pathway of homocysteine metabolism. In fungi, plants and bacteria, methionine can be processed to compounds such as methionol and/or 2-oxobutanoate." [MetaCyc:http\://biocyc.org/META/NEW-IMAGE?object=METHIONINE-DEG]
is_a: PW:0000048 ! methionine cycle/metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T13:56:22Z

[Term]
id: PW:0001303
name: steroid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of steroids." []
is_a: PW:0000248 ! isoprenoid metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T14:10:01Z

[Term]
id: PW:0001304
name: cholesterol metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of cholesterol, an essential component of cell membranes and lipid rafts and the precursor for the synthesis of steroid hormones and bile acids." []
is_a: PW:0001303 ! steroid metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T14:11:34Z

[Term]
id: PW:0001305
name: steroid hormone metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of steroid hormones." []
is_a: PW:0001303 ! steroid metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T14:14:55Z

[Term]
id: PW:0001306
name: altered steroid biosynthetic pathway
is_a: PW:0000751 ! altered isoprenoid biosynthetic pathway
is_a: PW:0001152 ! steroid biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-14T14:34:13Z

[Term]
id: PW:0001307
name: phosphatidylcholine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of phosphatidylcholine, an essential component of the membrane." [PMID:15749057, PMID:18204095]
is_a: PW:0000354 ! glycerophospholipid metabolic pathway
created_by: VPetri
creation_date: 2013-05-14T15:31:03Z

[Term]
id: PW:0001308
name: respiratory system disease pathway
is_a: PW:0000013 ! disease pathway
created_by: VPetri
creation_date: 2013-05-14T15:42:25Z

[Term]
id: PW:0001309
name: abscisic acid metabolic pathway
def: "Abscisic acid is a plant isoprenoid hormone important for development and stress responses." [PMID:22442388]
is_a: PW:0000248 ! isoprenoid metabolic pathway
created_by: VPetri
creation_date: 2013-05-20T11:34:20Z

[Term]
id: PW:0001310
name: abscisic acid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of abscisic acid, an important plant isoprenoid hormone." [PMID:22442388]
is_a: PW:0001309 ! abscisic acid metabolic pathway
created_by: VPetri
creation_date: 2013-05-20T11:45:49Z

[Term]
id: PW:0001311
name: sulfate assimilation pathway
def: "Sulfur, mostly found as inorganic sulfate can be taken up by plants, microorganisms and algae. Upon reduction to sulfide, is then incorporated into bioinorganic compounds. The underlying reactions and interactions constitute the sulfate assimilation pathway, best characterized in plants." [PMID:19876632]
is_a: PW:0000037 ! sulfur metabolic pathway
created_by: VPetri
creation_date: 2013-05-20T12:47:08Z

[Term]
id: PW:0001312
name: Nodal signaling pathway
def: "Nodal signaling pathway belongs to the transforming growth factor-beta superfamily and plays important roles during vertebrate embryogenesis where is involved in pattern formation and differentiation." [PMID:16838294]
is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway
created_by: VPetri
creation_date: 2013-05-20T14:12:57Z

[Term]
id: PW:0001313
name: transcription pathway via transcription factor mediated signaling
is_a: PW:0000100 ! transcription pathway
created_by: VPetri
creation_date: 2013-05-21T12:51:49Z

[Term]
id: PW:0001314
name: altered transcription pathway via transcription factor mediated signaling
is_a: PW:0000807 ! altered transcription pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2013-05-21T12:54:31Z

[Term]
id: PW:0001315
name: ascaroside metabolic pathway
def: "Those metabolic reactions involving ascaroside, a glycolipid containing the sugar ascarylose, found in nematodes." []
is_a: PW:0000733 ! glycosphingolipid metabolic pathway
created_by: VPetri
creation_date: 2013-05-21T13:47:21Z

[Term]
id: PW:0001316
name: ascaroside biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of ascaroside - a glycolipid containing the sugar ascarylose found in nematodes." []
is_a: PW:0001315 ! ascaroside metabolic pathway
created_by: VPetri
creation_date: 2013-05-21T13:48:54Z

[Term]
id: PW:0001317
name: cell cycle pathway
def: "The series of events, collectively known as the cell cycle, that underlie the replication of the genome and the segregation of chromosomes into daughter cells. The mitotic cell cycle pathway underlies the generation of new cells. The meiotic cell cycle pathway is a special type of cell division that takes place in germ cells." [Handbook:Essential Cell Biology]
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
created_by: VPetri
creation_date: 2013-05-22T09:56:40Z

[Term]
id: PW:0001318
name: cell cycle pathway, meiotic
def: "The series of events that take place in the germ cells resulting in the production of four non-identical haploid cells from each diploid cell that enters the cycle. Meiosis involves chromosomal pairing and exchange of DNA segments or recombination." [Handbook:Essential cell Biology]
is_a: PW:0001317 ! cell cycle pathway
created_by: VPetri
creation_date: 2013-05-22T10:19:26Z

[Term]
id: PW:0001319
name: toxic secondary metabolite biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of toxic secondary metabolite, known as mycotoxins, produced by some fungi, such as Fusarium. The mycotoxins they produce in cereal crops, such as species of fumonisins and trichothecenes, can affect humans and animals if present in food." [wikipedia:http\://en.wikipedia.org/wiki/Mycotoxin]
synonym: "mycotoxin biosynthetic pathway" RELATED []
is_a: PW:0001365 ! toxic secondary metabolite metabolic pathway
created_by: VPetri
creation_date: 2013-05-22T11:17:23Z

[Term]
id: PW:0001320
name: fumonisin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of fumonisin mycotoxins by members of Fusarium fungi." [wikipedia:http\://en.wikipedia.org/wiki/Fusarium]
is_a: PW:0001319 ! toxic secondary metabolite biosynthetic pathway
is_a: PW:0001367 ! fumonisin metabolic pathway
created_by: VPetri
creation_date: 2013-05-22T11:30:53Z

[Term]
id: PW:0001321
name: trichothecene biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of trichothecene mycotoxins by members of Fusarium fungi." [wikipedia:http\://en.wikipedia.org/wiki/Fusarium]
is_a: PW:0001319 ! toxic secondary metabolite biosynthetic pathway
is_a: PW:0001368 ! trichothecene metabolic pathway
created_by: VPetri
creation_date: 2013-05-22T11:31:27Z

[Term]
id: PW:0001322
name: deoxynivalenol biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of deoxynivalenol, a type B trichothecene produced by members of Fusarium fungi." [KEGG:http\://www.genome.jp/dbget-bin/www_bget?cpd\:C09747, wikipedia:http\://en.wikipedia.org/wiki/Deoxynivalenol]
synonym: "DON biosynthetic pathway" EXACT []
synonym: "vomitoxin biosynthetic pathway" RELATED []
is_a: PW:0001321 ! trichothecene biosynthetic pathway
created_by: VPetri
creation_date: 2013-05-22T11:36:22Z

[Term]
id: PW:0001323
name: mitochondrial translation pathway
def: "The translation pathway that takes place in the mitochondrion. The mitochondrial translation pathway utilizes 22 tRNAs which are encoded in the mitochondrial genome. The mitochondrial genome also encodes 2 ribosomal genes. A small set of mitochondrial proteins is translated in the mitochondrion by mitochondrially encoded genes. Most others are nuclearly encoded, synthesized on cytosolic ribosomes and then targeted to the organelle." [PMID:22258151, PMID:22729854]
is_a: PW:0000101 ! translation pathway
created_by: VPetri
creation_date: 2013-05-22T13:11:07Z

[Term]
id: PW:0001324
name: mitochondrial aminoacyl-tRNA biosynthetic pathway
def: "Aminoacyl-tRNA, or transfer RNA (tRNA) carries amino acids to ribosomes and is part of the translation pathway. tRNAs are specific for the amino acids with which they are associated. Their synthesis involves adenylation of the amino acid followed by its transfer; both steps require ATP. there are 22 tRNA genes encoded by the mitochondrial genome. Mutations in these genes have been implicated in a number of disorders and may affect various steps of tRNA biosynthesis." [PMID:22258151]
relationship: part_of PW:0001323 ! mitochondrial translation pathway
created_by: VPetri
creation_date: 2013-05-22T13:16:35Z

[Term]
id: PW:0001325
name: mitochondrial ribosome biogenesis pathway
relationship: part_of PW:0001323 ! mitochondrial translation pathway
created_by: VPetri
creation_date: 2013-05-22T13:40:51Z

[Term]
id: PW:0001326
name: altered mitochondrial translation pathway
is_a: PW:0001068 ! altered translation pathway
is_a: PW:0001323 ! mitochondrial translation pathway
created_by: VPetri
creation_date: 2013-05-22T13:59:43Z

[Term]
id: PW:0001327
name: altered mitochondrial aminoacyl-tRNA biosynthetic pathway
def: "Mutations in the mitochondrial tRNA genes are associated with a number of disorders. These mutations may affect steps in the biosynthesis of tRNA." [PMID:22258151]
is_a: PW:0001324 ! mitochondrial aminoacyl-tRNA biosynthetic pathway
is_a: PW:0001326 ! altered mitochondrial translation pathway
created_by: VPetri
creation_date: 2013-05-22T14:01:41Z

[Term]
id: PW:0001328
name: uridine diphosphate glucose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of uridine diphosphate glucose, a nucleotide sugar." [wikipedia:http\://en.wikipedia.org/wiki/UDP-glucose]
synonym: "UDP-glucose metabolic pathway" EXACT []
is_a: PW:0000055 ! nucleotide sugar metabolic pathway
created_by: VPetri
creation_date: 2013-05-22T14:27:01Z

[Term]
id: PW:0001329
name: guanosine diphosphate mannose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of  guanosine diphosphate mannose, a nucleotide sugar." [wikipedia:http\://en.wikipedia.org/wiki/GDP-mannose]
is_a: PW:0000055 ! nucleotide sugar metabolic pathway
created_by: VPetri
creation_date: 2013-05-22T14:32:54Z

[Term]
id: PW:0001330
name: receptor for advanced glycation end-products signaling pathway
def: "The receptor for advanced glycation end-products is a multi-ligand receptor whose signaling engages several downstream cascades. In addition to its pro-inflammatory role in innate immunity, it is also involved in tissue homeostasis and repair. It has been associated with a range of pathological states." [PMID:23103427]
synonym: "RAGE signaling pathway" EXACT []
is_a: PW:0000024 ! inflammatory response pathway
is_a: PW:0000819 ! signaling pathway in the innate immune response
created_by: VPetri
creation_date: 2013-05-22T14:54:54Z

[Term]
id: PW:0001331
name: RNA polymerase II transcription elongation pathway
def: "RNA polymerase II transcription elongation commences when the nascent transcript reaches about 25 residues. The general transcription factors are release and the RNA polymerase II alone carries out elongation of pre-mRNA transcript and proofreading. Splicing and alternative splicing, chromatin modification and remodeling and as necessary." [PMID:22975042, PMID:23000482, PMID:23046879]
relationship: part_of PW:0000127 ! RNA polymerase II transcription pathway
created_by: VPetri
creation_date: 2013-06-03T09:19:50Z

[Term]
id: PW:0001332
name: RNA polymerase II transcription termination pathway
def: "Termination of transcription is important for partitioning the genome and maintaining adequate expression of neighboring genes." [PMID:21487437]
relationship: part_of PW:0000127 ! RNA polymerase II transcription pathway
created_by: VPetri
creation_date: 2013-06-03T09:39:46Z

[Term]
id: PW:0001333
name: mitochondrial transcription pathway
def: "Transcription of mitochondrial DNA which encodes several genes involved in the oxidative phosphorylation pathway as well as the ribosomal and transfer RNA genes involved in their translation." [PMID:23632312]
is_a: PW:0000100 ! transcription pathway
created_by: VPetri
creation_date: 2013-06-03T09:44:20Z

[Term]
id: PW:0001334
name: non-coding RNA pathway
def: "Non-coding RNA are functional RNA molecules that are not translated into proteins. In addition to ribosomal and transfer RNA involved in protein translation many other small and long RNA are transcribed with important roles in the regulation of gene expression." [Cell March 2013:http\://www.cell.com/issue?pii=S0092-8674%2813%29X0007-8]
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
created_by: VPetri
creation_date: 2013-06-03T10:07:22Z

[Term]
id: PW:0001335
name: long non-coding RNA pathway
def: "Long non-coding RNA, of which there are several types, perform important regulatory roles whose function and mechanism are under investigation." [PMID:23463798]
is_a: PW:0001334 ! non-coding RNA pathway
created_by: VPetri
creation_date: 2013-06-03T10:15:04Z

[Term]
id: PW:0001336
name: CDP-choline pathway of phosphatidylcholine biosynthesis
def: "CDP-choline is one of the three distinct pathways of phosphatidylcholine biosynthesis. A second has been better studied in yeast while the third has only been identified in certain bacteria." [PMID:15749057]
synonym: "Kennedy pathway" RELATED []
is_a: PW:0000878 ! phosphatidylcholine biosynthetic pathway
created_by: VPetri
creation_date: 2013-06-03T11:26:24Z

[Term]
id: PW:0001337
name: chromatin modification/remodeling pathway
def: "Chromatin modification/remodeling plays a major role in the epigenetic control of gene expression. The dynamics of chromatin structure impacts on DNA replication, transcription and repair pathways. It includes the covalent modification of histones and DNA and the actions carried out by the ATP-dependent remodelers." [PMID:21655945, PMID:22203491, PMID:23085398, PMID:23524488]
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
relationship: part_of PW:0000099 ! DNA repair pathway
relationship: part_of PW:0000100 ! transcription pathway
relationship: part_of PW:0001317 ! cell cycle pathway
relationship: part_of PW:0001360 ! DNA damage response pathway
created_by: VPetri
creation_date: 2013-06-03T13:05:36Z

[Term]
id: PW:0001338
name: histone modification pathway
def: "The tails of histone proteins are subject to a wide array of modifications of which methylation and acetylation have been more thoroughly documented. The modified residues are recognized by particular proteins or readers, in turn acting upon their targets. The modifications are rendered reversible by the enzymes that carry out the reaction in the opposite direction, also referred to as erasers." [PMID:21655945, PMID:22203491, PMID:23085398]
is_a: PW:0001403 ! chromatin modification pathway
created_by: VPetri
creation_date: 2013-06-03T14:06:55Z

[Term]
id: PW:0001339
name: chromatin remodeling pathway
def: "Chromatin remodelers are large complexes that use the energy derived from ATP hydrolysis to promote nucleosome sliding, ejection or repositioning, histone exchange. Currently, there are four different families of chromatin remodeling complexes." [PMID:19355820, PMID:21655945, PMID:22203491, PMID:23085398, PMID:23524488]
is_a: PW:0001337 ! chromatin modification/remodeling pathway
created_by: VPetri
creation_date: 2013-06-03T14:14:26Z

[Term]
id: PW:0001340
name: DNA modification pathway
def: "DNA modification is a component of chromatin modification pathway. At least four DNA modification types are known. The modifications are recognized by specific readers and removed by eraser enzymes." [PMID:22894577]
is_a: PW:0001403 ! chromatin modification pathway
created_by: VPetri
creation_date: 2013-06-03T14:57:25Z

[Term]
id: PW:0001341
name: altered chromatin remodeling/modification pathway
def: "A chromatin remodeling/modification pathway that deviate from what its normal course should be. Aberrant chromatin remodeling and modification has been associated with various conditions, particularly cancer." [PMID:23127546, PMID:23524488]
is_a: PW:0001337 ! chromatin modification/remodeling pathway
created_by: VPetri
creation_date: 2013-06-03T15:02:51Z

[Term]
id: PW:0001342
name: sucrose biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of sucrose. The disaccharide is synthesized by plants and cyanobacteria." [wikipedia:http\://en.wikipedia.org/wiki/Sucrose]
is_a: PW:0000151 ! starch and sucrose metabolic pathway
created_by: VPetri
creation_date: 2013-06-04T11:18:11Z

[Term]
id: PW:0001343
name: phosphatidylglycerol metabolic process
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of phosphatidylglycerol. The molecule is a glycerophospholipid found in pulmonary surfactant." [PMID:21382416]
is_a: PW:0000354 ! glycerophospholipid metabolic pathway
created_by: VPetri
creation_date: 2013-06-04T11:47:01Z

[Term]
id: PW:0001344
name: cardiolipin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of cardiolipin. The molecule is derived from phosphatidylglycerol as an immature cardiolipin, further remodeled by phospholipases. Cardiolipin is important for a range of mitochondrial functions." [PMID:22014644]
is_a: PW:0001343 ! phosphatidylglycerol metabolic process
created_by: VPetri
creation_date: 2013-06-04T12:16:45Z

[Term]
id: PW:0001345
name: cardiolipin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of cardiolipin, a molecule important for mitochondrial function." [PMID:22014644]
is_a: PW:0001344 ! cardiolipin metabolic pathway
created_by: VPetri
creation_date: 2013-06-04T12:31:05Z

[Term]
id: PW:0001346
name: cholesterol transport pathway
def: "The pathways involved in the absorption and efflux of cholesterol." [PMID:17495606, PMID:20809793]
is_a: PW:0000103 ! transport pathway
created_by: VPetri
creation_date: 2013-06-04T12:45:55Z

[Term]
id: PW:0001347
name: altered cholesterol transport pathway
is_a: PW:0000545 ! altered transport pathway
is_a: PW:0001346 ! cholesterol transport pathway
created_by: VPetri
creation_date: 2013-06-04T12:49:29Z

[Term]
id: PW:0001348
name: ion transport pathway
is_a: PW:0000103 ! transport pathway
created_by: VPetri
creation_date: 2013-06-04T12:59:08Z

[Term]
id: PW:0001349
name: non-metal ion transport pathway
def: "The transport pathways of elements in group 1, 14, 15, 16 and 17 of the periodic table." [wikipedia:http\://en.wikipedia.org/wiki/Nonmetal]
is_a: PW:0001348 ! ion transport pathway
created_by: VPetri
creation_date: 2013-06-04T13:21:34Z

[Term]
id: PW:0001350
name: chloride ion transport pathway
def: "The transport pathway of chloride ion as carried out by chloride channels and transporters in cell and organelles." [PMID:20100480]
is_a: PW:0001349 ! non-metal ion transport pathway
created_by: VPetri
creation_date: 2013-06-04T13:30:44Z

[Term]
id: PW:0001351
name: altered non-metal ion transport pathway
is_a: PW:0001353 ! altered ion transport pathway
created_by: VPetri
creation_date: 2013-06-04T13:37:02Z

[Term]
id: PW:0001352
name: altered metal ion transport pathway
is_a: PW:0001353 ! altered ion transport pathway
created_by: VPetri
creation_date: 2013-06-04T13:37:22Z

[Term]
id: PW:0001353
name: altered ion transport pathway
is_a: PW:0001348 ! ion transport pathway
created_by: VPetri
creation_date: 2013-06-04T13:38:51Z

[Term]
id: PW:0001354
name: altered chloride ion transport pathway
def: "A chloride ion transport pathway that deviates from what its normal course should be. Aberrant chloride ion transport have been implicated in diseases. For instance, mutations in the ABC type transporter that functions as both a chloride channel and as a regulator of other transport pathways, have been implicated in two genetic disorders of which one is cystic fibrosis." [PMID:20100480]
is_a: PW:0001350 ! chloride ion transport pathway
is_a: PW:0001351 ! altered non-metal ion transport pathway
created_by: VPetri
creation_date: 2013-06-04T13:39:34Z

[Term]
id: PW:0001355
name: peroxisome proliferator-activated receptor signaling pathway
def: "Peroxisome proliferator-activated receptor signaling is initiated in response to binding several compounds within classes of lipids such as the eicosanoid, leukotriene, prostagladin, among others. The receptors form heterodimers with the retinoid X receptor, bind to specific DNA elements and regulate the expression of target genes. Deregulation of the pathway has been implicated in several conditions." [PMID:17132851, PMID:17317294]
synonym: "PPAR signaling pathway" EXACT []
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2013-06-05T08:45:28Z

[Term]
id: PW:0001356
name: altered peroxisome proliferator-activated receptor signaling pathway
def: "Deregulation of peroxisome proliferator-activated receptor signaling can affect innate immunity and play a role in metabolic diseases." [PMID:22704720]
synonym: "altered PPAR signaling pathway" EXACT []
is_a: PW:0000719 ! altered transcription factor mediated signaling pathway
is_a: PW:0001314 ! altered transcription pathway via transcription factor mediated signaling
is_a: PW:0001355 ! peroxisome proliferator-activated receptor signaling pathway
created_by: VPetri
creation_date: 2013-06-05T09:29:37Z

[Term]
id: PW:0001357
name: coenzyme A metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of coenzyme A, an  important for fatty acids, pyruvate and citric acid metabolic pathways." [wikipedia:http\://en.wikipedia.org/wiki/Coenzyme_A]
is_a: PW:0000167 ! pantothenic acid metabolic pathway
created_by: VPetri
creation_date: 2013-06-06T10:13:36Z

[Term]
id: PW:0001358
name: coenzyme A biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of coenzyme A. The five step reaction pathway requires pantothenate (vitamin B5) and cysteine as precursors." [PMID:11923312]
is_a: PW:0001357 ! coenzyme A metabolic pathway
created_by: VPetri
creation_date: 2013-06-06T10:18:42Z

[Term]
id: PW:0001359
name: altered nucleotide excision repair pathway
def: "A nucleotide excision repair pathway that deviates from what its normal course should be. Defects in this repair pathway have been associated with cancer and premature aging." [PMID:22824526]
synonym: "altered NER pathway" RELATED []
is_a: PW:0000130 ! nucleotide excision repair pathway
is_a: PW:0000666 ! altered single-strand DNA repair pathway
created_by: VPetri
creation_date: 2013-06-10T09:38:04Z

[Term]
id: PW:0001360
name: DNA damage response pathway
def: "The response mechanism/pathways that assure the maintenance of genomic integrity. This involves detection of DNA damage, signaling and amplification of the signal leading to activation of effectors and resulting in repair of damage, cell cycle arrest or, if necessary, cell death. Such  response mechanism/pathways may operate collectively with some of their components being shared." [PMID:19847258]
synonym: "DDR pathway" RELATED []
is_a: PW:0000085 ! pathway pertinent to DNA replication, cell cycle, DNA repair and maintenance of genomic integrity, RNA and protein biosynthesis
created_by: VPetri
creation_date: 2013-06-11T11:03:38Z

[Term]
id: PW:0001361
name: ATM signaling pathway
def: "The ATM serine/threonine kinase mediated signaling plays a major role in the response to DNA double strand breaks (DSB). Following lesion sensing by the MRN complex, ATM gets activated. Active ATM phosphorylates itself and targets resulting in triggering if  DNA repair, cell cycle checkpoint and signaling pathways. While ATM signaling is best documented for its role in DSB responses, evidence accumulates that it functions in range of other, DNA damage unrelated, responses." [PMID:23486281, PMID:23532176]
is_a: PW:0001194 ! serine/threonine-specific kinase mediated signaling pathway
relationship: part_of PW:0001360 ! DNA damage response pathway
created_by: VPetri
creation_date: 2013-06-11T11:25:06Z

[Term]
id: PW:0001362
name: ATR signaling pathway
def: "The ATR serine/threonine kinase mediated signaling responds to several kinds of DNA damage, of which single-stranded DNA (ssDNA) exerts a key role. ATR acting on its substrates prevents the cell from erroneous mitotic entry and also promotes homologous recombination repair pathway." [PMID:20947357, PMID:21615334, PMID:22417748]
is_a: PW:0001194 ! serine/threonine-specific kinase mediated signaling pathway
relationship: part_of PW:0001360 ! DNA damage response pathway
created_by: VPetri
creation_date: 2013-06-11T11:25:59Z

[Term]
id: PW:0001363
name: lactose metabolic pathway
def: "Those metabolic reactions involving lactose, a disaccharide found in milk." [Wikipedia:http\://en.wikipedia.org/wiki/Lactose]
is_a: PW:0000005 ! carbohydrate metabolic pathway
created_by: VPetri
creation_date: 2013-06-11T13:14:11Z

[Term]
id: PW:0001364
name: lactose degradation pathway
def: "The breaking down of lactose to its constituent sugars." [Wikipedia:http\://en.wikipedia.org/wiki/Lactose]
is_a: PW:0001363 ! lactose metabolic pathway
created_by: VPetri
creation_date: 2013-06-11T13:17:06Z

[Term]
id: PW:0001365
name: toxic secondary metabolite metabolic pathway
def: "Toxic secondary metabolites, also known as mycotoxins, are natural toxins produced by organisms that belong to the fungi kingdom. They can contaminate crops and if ingested, they can cause sickness or death." [PMID:18258326]
synonym: "mycotoxin metabolic pathway" RELATED []
is_a: PW:0000147 ! metabolic pathway of secondary metabolites
created_by: VPetri
creation_date: 2013-06-11T13:37:37Z

[Term]
id: PW:0001366
name: aflatoxin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, transport and/or degradation of aflatoxins. Aflatoxins are potent toxic secondary metabolites that contaminate grain and nut crops. Of the four types of aflatoxin, aflatoxin B1 is the most toxic one." [PMID:19010433]
is_a: PW:0001365 ! toxic secondary metabolite metabolic pathway
created_by: VPetri
creation_date: 2013-06-11T13:46:23Z

[Term]
id: PW:0001367
name: fumonisin metabolic pathway
is_a: PW:0001365 ! toxic secondary metabolite metabolic pathway
created_by: VPetri
creation_date: 2013-06-11T14:09:22Z

[Term]
id: PW:0001368
name: trichothecene metabolic pathway
is_a: PW:0001365 ! toxic secondary metabolite metabolic pathway
created_by: VPetri
creation_date: 2013-06-11T14:09:45Z

[Term]
id: PW:0001369
name: shikimate metabolic pathway
def: "The shikimate pathway is the  metabolic route for the production of aromatic amino acids in plants. Seven reactions catalyzed by six enzymes result in the production of chorismate, the major branch point metabolite. Chorismate is the precursor for the biosynthesis of phenylalanine, tryptophan and tyrosine." [PMID:20817774]
is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway
created_by: VPetri
creation_date: 2013-06-19T09:13:02Z

[Term]
id: PW:0001370
name: chorismate metabolic pathway
def: "Chorismate, the major branch point metabolite of shikimate pathway is the precursor for the biosynthesis of aromatic amino acids phenylalanine, tryptophan and tyrosine in plants." [PMID:20817774]
is_a: PW:0001369 ! shikimate metabolic pathway
created_by: VPetri
creation_date: 2013-06-19T09:31:50Z

[Term]
id: PW:0001371
name: basic helix-loop-helix signaling pathway
def: "Basic helix-loop-helix proteins represent a large superfamily of transcription factors that regulate the expression of genes involved in growth and development as well as environmental responses. Phylogenetically, they are classified into six clades of which the sixth, also referred to as clade F only contains plant genes." [PMID:20219281]
is_a: PW:0000716 ! transcription factor mediated signaling pathway
is_a: PW:0001313 ! transcription pathway via transcription factor mediated signaling
created_by: VPetri
creation_date: 2013-06-19T11:06:19Z

[Term]
id: PW:0001372
name: Inhibitor of DNA binding signaling pathway
def: "The inhibitor of DNA binding (ID) family belongs to the basic helix-loop-helix superfamily of transcription factor that regulate cell growth and differentiation. They lack the DNA binding domain and exert their gene expression regulatory function through the interaction with other transcription factors. They also appear to play a role in malignant biology; in neural cancers, deregulated activity has been associated with tumor progression." [PMID:15013218, PMID:15530557]
synonym: "ID signaling pathway" EXACT []
is_a: PW:0001371 ! basic helix-loop-helix signaling pathway
created_by: VPetri
creation_date: 2013-06-19T11:37:26Z

[Term]
id: PW:0001373
name: altered inhibitor of DNA binding signaling pathway
def: "An inhibitor of DNA signaling pathway that deviates from what its normal course should be. In neural cancers, deregulated activity has been associated with tumor progression." [PMID:15013218]
is_a: PW:0001372 ! Inhibitor of DNA binding signaling pathway
is_a: PW:0001374 ! altered basic helix-loop-helix signaling pathway
created_by: VPetri
creation_date: 2013-06-19T12:12:02Z

[Term]
id: PW:0001374
name: altered basic helix-loop-helix signaling pathway
def: "A  basic helix-loop-helix signaling pathway that deviates from its normal course should be." []
is_a: PW:0000719 ! altered transcription factor mediated signaling pathway
is_a: PW:0001314 ! altered transcription pathway via transcription factor mediated signaling
is_a: PW:0001371 ! basic helix-loop-helix signaling pathway
created_by: VPetri
creation_date: 2013-06-19T12:21:30Z

[Term]
id: PW:0001375
name: nicotinamide adenine dinucleotide biosynthesis, the salvage pathway
def: "Nicotinamide adenine dinucleotide biosynthetic pathway via 'salvageable precursors'." [PMID:18429699]
is_a: PW:0000219 ! nicotinamide adenine dinucleotide biosynthetic pathway
created_by: VPetri
creation_date: 2013-06-19T12:47:03Z

[Term]
id: PW:0001376
name: formaldehyde assimilation pathway
def: "Methane oxidation by metanotrophs produces formaldehyde which assimilated to form metabolite subsequently used for the biosynthesis of multi-carbon compounds. Two pathways of formaldehyde assimilation are known. Both pathways are cyclic." [BioCyc:http\://www.biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-1861]
is_a: PW:0000068 ! methane metabolic pathway
created_by: VPetri
creation_date: 2013-06-19T12:54:29Z

[Term]
id: PW:0001377
name: serine pathway of formaldehyde assimilation
def: "The serine pathway is one of two pathways of formaldehyde assimilation resulting in a three-carbon intermediate." [BioCyc:http\://www.biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-1861]
is_a: PW:0001376 ! formaldehyde assimilation pathway
created_by: VPetri
creation_date: 2013-06-19T13:00:01Z

[Term]
id: PW:0001378
name: RuMP pathway of formaldehyde assimilation
def: "The RuMP pathway, or RuMP cycle, is one of two pathways of formaldehyde assimilation resulting in a three-carbon intermediate." [BioCyc:http\://www.biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-1861]
synonym: "RuMP cycle of formaldehyde assimilation" EXACT []
is_a: PW:0001376 ! formaldehyde assimilation pathway
created_by: VPetri
creation_date: 2013-06-19T13:25:58Z

[Term]
id: PW:0001379
name: octane oxidation pathway
def: "Those metabolic reactions involved in the oxidation of octane and found in some bacteria. The final product can be utilized as a source of carbon and energy." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=P221-PWY]
is_a: PW:0000033 ! energy metabolic pathway
created_by: VPetri
creation_date: 2013-06-19T13:32:23Z

[Term]
id: PW:0001380
name: glutamate degradation pathway I
def: "Those metabolic reactions involved in the deamination pathway of glutamate degradation that is found in microorganisms and plants. It results in ammonia and the 2-oxoglutarate compound which is fed into the citric acid cycle." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=GLUTAMATE-DEG1-PWY]
is_a: PW:0001263 ! glutamic acid/glutamate degradation pathway
created_by: VPetri
creation_date: 2013-06-19T14:06:34Z

[Term]
id: PW:0001381
name: glutamate degradation pathway II
def: "Those metabolic reactions involved in the glutamate degradation pathway II found in certain bacteria." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=GLUTDEG-PWY]
is_a: PW:0001263 ! glutamic acid/glutamate degradation pathway
created_by: VPetri
creation_date: 2013-06-19T14:10:31Z

[Term]
id: PW:0001382
name: glutamate degradation pathway III
def: "Those metabolic reactions involved in glutamate degradation pathway III which proceeds via 4-aminobutanoate (GABA) and is found in humans and other mammals." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=GLUTDEG-PWY]
synonym: "GABA shunt pathway" RELATED []
is_a: PW:0001263 ! glutamic acid/glutamate degradation pathway
created_by: VPetri
creation_date: 2013-06-19T14:23:45Z

[Term]
id: PW:0001383
name: glutamate degradation pathway IV
def: "Those metabolic reaction involved in glutamate degradation pathway IV. It proceeds via 4-aminobutanoate (GABA), like degradation pathway III, but is found in plants." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-4321]
is_a: PW:0001263 ! glutamic acid/glutamate degradation pathway
created_by: VPetri
creation_date: 2013-06-19T14:27:40Z

[Term]
id: PW:0001384
name: glutamate degradation pathway V
def: "Those metabolic reactions involved in glutamate degradation pathway V, a fermentation pathway of glutamate degradation. Glutamate degradation pathway V proceeds via hydroxyglutarate and is one of the major pathways of glutamate fermentation." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=P162-PWY]
is_a: PW:0001385 ! glutamate fermentation pathway
created_by: VPetri
creation_date: 2013-06-19T14:35:18Z

[Term]
id: PW:0001385
name: glutamate fermentation pathway
def: "Certain anaerobic bacteria are capable of fermenting amino acids. While at least one fermentation pathway is known for every amino acid, several have been reported for glutamate." [PMID:11759672]
is_a: PW:0001263 ! glutamic acid/glutamate degradation pathway
created_by: VPetri
creation_date: 2013-06-19T15:15:10Z

[Term]
id: PW:0001386
name: glutamate degradation pathway VII
def: "Those metabolic reactions involved in glutamate degradation pathway VII, a fermentation pathway of glutamate degradation. It is a methylaspartate pathway and a major route of glutamate fermentation, together with degradation pathway VI and VIII." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=GLUDEG-II-PWY]
is_a: PW:0001385 ! glutamate fermentation pathway
created_by: VPetri
creation_date: 2013-06-19T15:24:31Z

[Term]
id: PW:0001387
name: glutamate degradation pathway VI
def: "Those metabolic reactions involved in glutamate degradation pathway VI, a fermentation pathway of glutamate degradation. It is a methylaspartate pathway and a major route of glutamate fermentation, together with degradation pathway VII and VIII." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5087]
is_a: PW:0001385 ! glutamate fermentation pathway
created_by: VPetri
creation_date: 2013-06-19T15:24:53Z

[Term]
id: PW:0001388
name: glutamate degradation pathway VIII
def: "Those metabolic reactions involved in glutamate degradation pathway VIII, a fermentation pathway of glutamate degradation. It is a methylaspartate pathway and a major route of glutamate fermentation, together with degradation pathway VI and VII." [BioCyc:http\://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5088]
is_a: PW:0001385 ! glutamate fermentation pathway
created_by: VPetri
creation_date: 2013-06-19T15:49:47Z

[Term]
id: PW:0001389
name: glutamate degradation pathway IX
is_a: PW:0001263 ! glutamic acid/glutamate degradation pathway
created_by: VPetri
creation_date: 2013-06-19T15:55:54Z

[Term]
id: PW:0001390
name: starch biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of starch, a carbohydrate produced by all green plants as an energy store." [Wikipedia:http\://en.wikipedia.org/wiki/Starch]
is_a: PW:0000151 ! starch and sucrose metabolic pathway
is_a: PW:0001391 ! starch and cellulose metabolic pathway
created_by: VPetri
creation_date: 2013-06-20T09:20:52Z

[Term]
id: PW:0001391
name: starch and cellulose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of starch and cellulose, two similar polymers produced and used by green plants. Both are made from glucose repeat units that differ in their orientation." [Online:http\://pslc.ws/macrog/starlose.htm]
is_a: PW:0000005 ! carbohydrate metabolic pathway
created_by: VPetri
creation_date: 2013-06-20T09:24:14Z

[Term]
id: PW:0001392
name: cellulose biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of cellulose, an important structural components of cell wall of green plants, many forms of algae and some fungus-like microorganisms." [Wikipedia:http\://en.wikipedia.org/wiki/Cellulose]
is_a: PW:0001391 ! starch and cellulose metabolic pathway
created_by: VPetri
creation_date: 2013-06-20T09:32:33Z

[Term]
id: PW:0001393
name: starch and cellulose biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of starch and cellulose, two related polymers." []
is_a: PW:0001391 ! starch and cellulose metabolic pathway
created_by: VPetri
creation_date: 2013-06-20T09:32:56Z

[Term]
id: PW:0001394
name: terpene and terpenoid biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of terpene and terpenoid, large classes of related organic compounds. Modified terpenes, via oxidation or re-arrangement of the carbon skeleton, the resulting compounds are generally referred to as terpenoids." [Wikipedia:http\://en.wikipedia.org/wiki/Terpene]
is_a: PW:0001397 ! terpene and terpenoid metabolic pathway
created_by: VPetri
creation_date: 2013-06-20T14:12:23Z

[Term]
id: PW:0001395
name: terpene biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of terpene, a large class or organic compounds produced by a variety of plants and some insects." [Wikipedia:http\://en.wikipedia.org/wiki/Terpene]
is_a: PW:0001394 ! terpene and terpenoid biosynthetic pathway
created_by: VPetri
creation_date: 2013-06-20T14:16:34Z

[Term]
id: PW:0001396
name: monoterpene biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of monoterpene, a class of terpene composed of two isoprene units." [Wikipedia:http\://en.wikipedia.org/wiki/Terpene]
is_a: PW:0001395 ! terpene biosynthetic pathway
created_by: VPetri
creation_date: 2013-06-20T14:18:52Z

[Term]
id: PW:0001397
name: terpene and terpenoid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of terpene and terpenoid, large classes of related organic compounds." []
is_a: PW:0000147 ! metabolic pathway of secondary metabolites
created_by: VPetri
creation_date: 2013-06-20T14:21:16Z

[Term]
id: PW:0001398
name: terpene and terpenoid degradation pathway
is_a: PW:0001397 ! terpene and terpenoid metabolic pathway
created_by: VPetri
creation_date: 2013-06-20T14:23:32Z

[Term]
id: PW:0001399
name: terpene degradation pathway
is_a: PW:0001398 ! terpene and terpenoid degradation pathway
created_by: VPetri
creation_date: 2013-06-20T14:24:06Z

[Term]
id: PW:0001400
name: terpenoid degradation pathway
is_a: PW:0001398 ! terpene and terpenoid degradation pathway
created_by: VPetri
creation_date: 2013-06-20T14:24:24Z

[Term]
id: PW:0001401
name: diterpene biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of diterpene, a class of terpene composed of four isoprene units." [Wikipedia:http\://en.wikipedia.org/wiki/Terpene]
is_a: PW:0001395 ! terpene biosynthetic pathway
created_by: VPetri
creation_date: 2013-06-20T14:27:06Z

[Term]
id: PW:0001402
name: momilactone biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of momilactone - a diterpene produced by rice. Momilactone A and B can act as potent phytoalexins and allelochemicals" [PMID:21620514, Wikipedia:http\://en.wikipedia.org/wiki/Momilactone_B]
is_a: PW:0001401 ! diterpene biosynthetic pathway
created_by: VPetri
creation_date: 2013-06-20T14:31:15Z

[Term]
id: PW:0001403
name: chromatin modification pathway
def: "The pathway of chromatin - DNA  and constituent histones, modification mediated by writers and recognized by readers which in turn, act upon their effectors. The modifications are removed by erasers. Mutations in the writer, reader or eraser categories are known to be implicated in cancer." [PMID:22770212, PMID:22894577]
is_a: PW:0001337 ! chromatin modification/remodeling pathway
created_by: VPetri
creation_date: 2013-06-25T10:34:08Z

[Term]
id: PW:0001404
name: altered chromatin modification pathway
def: "A chromatin modification pathway that deviate from what its normal course should be. Mutations in the writer, reader or eraser categories of chromatin modification have been implicated in cancer." [PMID:22894577]
is_a: PW:0001341 ! altered chromatin remodeling/modification pathway
is_a: PW:0001403 ! chromatin modification pathway
created_by: VPetri
creation_date: 2013-06-25T10:51:36Z

[Term]
id: PW:0001405
name: altered chromatin remodeling pathway
def: "A chromatin remodeling pathway that deviates from what its normal course should be. Mutations in members of the various chromatin remodeling families have been implicated in cancer." [PMID:22894577]
is_a: PW:0001339 ! chromatin remodeling pathway
is_a: PW:0001341 ! altered chromatin remodeling/modification pathway
created_by: VPetri
creation_date: 2013-06-25T10:58:35Z

[Term]
id: PW:0001406
name: SWI/SNF family mediated chromatin remodeling pathway
def: "The SWI/SNF (switching defective/sucrose nonfermenting) family of remodelers has initially been purified from Saccharomyces cerevisiae. In  mammals, two complexes are comprised of one of two mutually exclusive catalytic ATPase subunits along with a set of conserved core subunits and variant subunits. The SWI/SNF is involved in nucleosome sliding and ejection." [PMID:19355820, PMID:21654818]
is_a: PW:0001339 ! chromatin remodeling pathway
created_by: VPetri
creation_date: 2013-06-25T13:27:31Z

[Term]
id: PW:0001407
name: ISWI family mediated chromatin remodeling pathway
def: "The ISWI (imitation switch) family of remodelers has initially been purified from Drosophila melanogaster. Eukaryotic assemble several ISWI complexes using one or two different catalytic subunits. Many complexes function to promote chromatin assembly and repression of transcription. Overall, the pathway is important for DNA replication and repair along with the regulation of transcription." [PMID:19355820]
is_a: PW:0001339 ! chromatin remodeling pathway
created_by: VPetri
creation_date: 2013-06-25T13:37:13Z

[Term]
id: PW:0001408
name: INO80 family mediated chromatin remodeling pathway
def: "The INO80 (inositol requiring 80) family of remodelers has been initially purified from Saccharomyces cerevisiae. It promotes transcriptional activation and DNA repair." [PMID:19355820]
is_a: PW:0001339 ! chromatin remodeling pathway
created_by: VPetri
creation_date: 2013-06-25T13:45:06Z

[Term]
id: PW:0001409
name: CHD family mediated chromatin remodeling pathway
def: "The CHD (chromodomain, helicase, DNA binding) family of remodelers has initially been purified from Xenopus laevis. Some CHD remodelers are involved in sliding and ejection of nucleosome to promote transcription while others may have repressive roles." []
is_a: PW:0001339 ! chromatin remodeling pathway
created_by: VPetri
creation_date: 2013-06-25T13:49:53Z

[Term]
id: PW:0001410
name: altered DNA modification pathway
def: "A DNA modification pathway that deviates from what its normal course should be. Mutations in the writer, reader or eraser categories of DNA modification have been implicated in several developmental abnormalities and human malignancies." [PMID:22770212]
is_a: PW:0001340 ! DNA modification pathway
is_a: PW:0001404 ! altered chromatin modification pathway
created_by: VPetri
creation_date: 2013-06-25T14:06:48Z

[Term]
id: PW:0001411
name: altered histone modification pathway
def: "A histone modification pathway that deviates from what its normal course should be. Mutations in the writer, reader or eraser categories of several types of histone modification have been implicated in various forms of cancer." [PMID:22770212]
is_a: PW:0001338 ! histone modification pathway
is_a: PW:0001404 ! altered chromatin modification pathway
created_by: VPetri
creation_date: 2013-06-25T14:09:30Z

[Term]
id: PW:0001412
name: nervous system disease pathway
def: "Any disease that affects the central or peripheral nervous system. It includes brain, neurological, neurodegenerative, cerebrovascular disorders, syndromes, dystrophies and others. However, mental or neuropsychiatric disorders are not included." [MeSH:MeSH Descriptor]
is_a: PW:0000013 ! disease pathway
created_by: VPetri
creation_date: 2013-07-01T09:53:15Z

[Term]
id: PW:0001413
name: liver disease pathway
def: "The congenital and acquired diseases affecting the kidney." []
is_a: PW:0000013 ! disease pathway
created_by: VPetri
creation_date: 2013-07-01T10:08:33Z

[Term]
id: PW:0001414
name: brain disease pathway
def: "The congenital and acquired diseases affecting the brain, including but not limited to the cerebral cortex, basal ganglia, thalamus and hypothalamus, brain stem, cerebellum." [MeSH:MeSH descriptor]
is_a: PW:0001412 ! nervous system disease pathway
created_by: VPetri
creation_date: 2013-07-01T10:10:37Z

[Term]
id: PW:0001415
name: Zellweger syndrome pathway
def: "A cerebro-hepato-renal phenotype caused by mutations in genes involved in the peroxisome biogenesis pathway." [MeSH:MeSH descriptor]
is_a: PW:0000300 ! renal system disease, renal disorder pathway
is_a: PW:0001413 ! liver disease pathway
is_a: PW:0001414 ! brain disease pathway
created_by: VPetri
creation_date: 2013-07-01T10:12:52Z

[Term]
id: PW:0001416
name: Leigh syndrome pathway
def: "A neurometabolic disorder affecting the central nervous system caused by defects in mitochondrial and/or nuclear genes involved in energy metabolic pathways." [MeSH:MeSH descriptor]
is_a: PW:0001414 ! brain disease pathway
created_by: VPetri
creation_date: 2013-07-01T10:17:22Z

[Term]
id: PW:0001417
name: Canavan disease pathway
def: "A rare autosomal recessive condition characterized by degeneration of the nervous system due to white matter vacuolization and demeylination. It results from defects in ASPA, aspartoacylase gene involved in several amino acid metabolic pathways." [MeSH:MeSH descriptor]
synonym: "Canavan-Van Bogaert-Bertrand disease pathway" EXACT []
is_a: PW:0000014 ! neurodegenerative disease pathway
is_a: PW:0001414 ! brain disease pathway
created_by: VPetri
creation_date: 2013-07-01T10:30:56Z

[Term]
id: PW:0001418
name: abciximab drug pathway
def: "The pharmacokinetics and pharmacodynamics of abciximab, an integrin receptor antagonist used as a platelet aggregation inhibitor. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [ATC/DDD Index:http\://www.whocc.no/atc_ddd_index/?code=B01AC13, wikipedia:http\://en.wikipedia.org/wiki/Abciximab]
is_a: PW:0000922 ! blood and blood forming organs drug pathway
created_by: VPetri
creation_date: 2013-07-01T11:09:26Z

[Term]
id: PW:0001419
name: abciximab pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of anciximab, a platelet aggregation inhibitor. Genetic variations can result in changes in the availability of the drug." []
is_a: PW:0001418 ! abciximab drug pathway
created_by: VPetri
creation_date: 2013-07-01T11:13:54Z

[Term]
id: PW:0001420
name: abciximab pharmacodynamics pathway
def: "The pathway of abciximab-target interaction and of the biochemical or physiological responses to drug. Abciximab is an antagonist of the integrin alpha2b/beta3 complex found on platelets. Genetic variations can cause differences in the response of the organism to the drug." []
is_a: PW:0001418 ! abciximab drug pathway
created_by: VPetri
creation_date: 2013-07-01T11:15:29Z

[Term]
id: PW:0001421
name: kanamycin drug pathway
def: "The pharmacokinetics and pharmacodynamics of kanamycin, an aminoglycoside antibiotic that inhibits bacterial protein synthesis. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [ATC/DDD Index:http\://www.whocc.no/atc_ddd_index/?code=A07AA08, wikipedia:http\://en.wikipedia.org/wiki/Kanamycin]
is_a: PW:0000996 ! anti-infective drug pathway
created_by: VPetri
creation_date: 2013-07-01T11:51:37Z

[Term]
id: PW:0001422
name: kanamycin pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of kanamycin - an antibiotic that interferes with bacterial protein synthesis. Genetic variations can result in changes in the availability of the drug." []
is_a: PW:0001421 ! kanamycin drug pathway
created_by: VPetri
creation_date: 2013-07-01T12:02:46Z

[Term]
id: PW:0001423
name: kanamycin pharmacodynamics pathway
def: "The pathway of kanamycin-target interaction and of the biochemical or physiological responses to drug. Kanamycin interferes with bacterial protein synthesis and is used in the treatment of several infections caused by both Gram-negative and Gram-positive bacteria. Genetic variations can cause differences in the response of the organism to the drug." []
is_a: PW:0001421 ! kanamycin drug pathway
created_by: VPetri
creation_date: 2013-07-01T12:04:30Z

[Term]
id: PW:0001424
name: neviparine drug pathway
def: "The pharmacokinetics and pharmacodynamics of neviparine, a non-nucleoside reverse transcriptase inhibitor used in the treatment of HIV type 1. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/search/pathwaysByCategory.action#pathwayCategories\:981478748]
is_a: PW:0000996 ! anti-infective drug pathway
created_by: VPetri
creation_date: 2013-07-01T12:10:20Z

[Term]
id: PW:0001425
name: neviparine pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of neviparine, a reverse transcriptase inhibitor. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165950411]
is_a: PW:0001424 ! neviparine drug pathway
created_by: VPetri
creation_date: 2013-07-01T12:30:46Z

[Term]
id: PW:0001426
name: neviparine pharmacodynamics pathway
def: "The pathway of neviaparine-target interaction and of the biochemical or physiological responses to drug. Neviparine is a non-nucleoside reverse transcriptase inhibitor used in combination with other antiretroviral drugs  for the treatment of HIV type. Genetic variations can cause differences in the response of the organism to the drug." [PgarmGKB:http\://www.pharmgkb.org/pathway/PA165950411]
is_a: PW:0001424 ! neviparine drug pathway
created_by: VPetri
creation_date: 2013-07-01T12:31:48Z

[Term]
id: PW:0001427
name: amikacin drug pathway
def: "The pharmacokinetics and pharmacodynamics of amikacin, an aminoglycoside antibiotic that inhibits bacterial protein synthesis. It is used for the treatment of infections induced by Gram-negative bacteria. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [ATC/DDD Index:http\://www.whocc.no/atc_ddd_index/?code=J01GB06, wikipedia:http\://en.wikipedia.org/wiki/Amikacin]
is_a: PW:0000996 ! anti-infective drug pathway
created_by: VPetri
creation_date: 2013-07-01T12:53:28Z

[Term]
id: PW:0001428
name: amikacin pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of amikacin, an antibiotic used for the treatment of infections induced by Gram-negative bacteria. Genetic variations can result in changes in the availability of the drug." []
is_a: PW:0001427 ! amikacin drug pathway
created_by: VPetri
creation_date: 2013-07-01T12:55:58Z

[Term]
id: PW:0001429
name: amikacin pharmacodynamics pathway
def: "The pathway of amikacin-target interaction and of the biochemical or physiological responses to drug. Amikacin inhibits bacterial protein synthesis and is used for the treatment of infections induced by Gram-negative bacteria. Genetic variations can cause differences in the response of the organism to the drug." []
is_a: PW:0001427 ! amikacin drug pathway
created_by: VPetri
creation_date: 2013-07-01T12:57:16Z

[Term]
id: PW:0001430
name: lamivudine drug pathway
def: "The pharmacokinetics and pharmacodynamics of lamivudine, a reverse transcriptase enzyme inhibitor used for the treatment of HIV type 1 and 2 and Hepatitis B virus. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [ATC/DDD Index:http\://www.whocc.no/atc_ddd_index/?code=J05AF05, PharmGKB:http\://www.pharmgkb.org/pathway/PA165860384]
is_a: PW:0000996 ! anti-infective drug pathway
created_by: VPetri
creation_date: 2013-07-01T13:09:51Z

[Term]
id: PW:0001431
name: lamivudine pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination of lamivudine, a reverse transcriptase inhibitor used for the treatment of several virally induced diseases. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165860384]
is_a: PW:0001430 ! lamivudine drug pathway
created_by: VPetri
creation_date: 2013-07-01T13:12:34Z

[Term]
id: PW:0001432
name: lamivudine pharmacodynamics pathway
def: "The pathway of lamivudine-target interaction and of the biochemical or physiological responses to drug. Lamivudine is a a reverse transcriptase enzyme inhibitor used for the treatment of HIV typ1 and 2 and Hepatitis B. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165860384]
is_a: PW:0001430 ! lamivudine drug pathway
created_by: VPetri
creation_date: 2013-07-01T13:17:12Z

[Term]
id: PW:0001433
name: gentamicin drug pathway
def: "The pharmacokinetics and pharmacodynamics of gentamicin, an antibiotic that inhibits bacterial protein synthesis. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [ATC/DDD Index:http\://www.whocc.no/atc_ddd_index/?code=J01GB03]
is_a: PW:0000996 ! anti-infective drug pathway
created_by: VPetri
creation_date: 2013-07-01T13:22:06Z

[Term]
id: PW:0001434
name: toxin and toxicant response pathway
def: "The responses triggered by exposure to a toxin or a toxicant, a poisonous substance naturally produced by an organism or made by humans, respectively. A toxicant can be a poison, such as a pesticide. It can also be a compound for use in certain applications, the exposure to which, if in high enough doses, may be toxic. Inflammatory responses, various types of cell death, changes in gene and protein expression can be induced upon exposure." [Wikipedia:https\://en.wikipedia.org/wiki/Toxin]
is_a: PW:0000124 ! cellular detoxification pathway
created_by: VPetri
creation_date: 2013-07-10T09:32:50Z

[Term]
id: PW:0001435
name: nanomaterial response pathway
def: "A pathway triggered by exposure to a nanomaterial. Nanomaterials, such as fullerenes and inorganic nanoparticles are increasingly being used in a broad range of applications. However, in a dose-dependent manner, they may exert toxic effects that affect cellular pathways and processes and elicit defense mechanisms." [Wikipedia:http\://en.wikipedia.org/wiki/Nanomaterials]
is_a: PW:0001434 ! toxin and toxicant response pathway
created_by: VPetri
creation_date: 2013-07-10T10:09:18Z

[Term]
id: PW:0001436
name: carbon nanotube response pathway
def: "A pathway triggered by exposure to carbon nanotube (CNT), an allotrope of carbon of the fullerene structural family. CNTs have a very broad range of applications but can also exert toxic effects. Pulmonary toxicity possibly via reactive oxygen species, inhibition of potassium channels and DNA repair are some of the potential mechanisms of CNT genotoxicity. Various forms of cell death and inflammatory responses are triggered in response to CNT." [PMID:22720979, PMID:23751779, PMID:23770455]
synonym: "CNT response pathway" EXACT []
is_a: PW:0001435 ! nanomaterial response pathway
created_by: VPetri
creation_date: 2013-07-10T10:33:41Z

[Term]
id: PW:0001437
name: titanium dioxide nanoparticle response pathway
def: "A pathway triggered by exposure to titanium dioxide nanoparticle (nano-TiO2). Nano-TiO2 has a broad range of applications but studies indicate that under conditions of long and high dose exposure, it can exert cytotoxic and genotoxic effects. Nano-TiO2 has been shown to induce inflammation, oxidative stress and MAP kinase activity." [PMID:23380242]
synonym: "nano-TiO2 response pathway" EXACT []
is_a: PW:0001435 ! nanomaterial response pathway
created_by: VPetri
creation_date: 2013-07-10T13:08:48Z

[Term]
id: PW:0001438
name: polycyclic aromatic hydrocarbon metabolic pathway
def: "Those metabolic reactions involved in the uptake, modification and elimination of polycyclic aromatic hydrocarbons (PAHs), a class of compounds, members of which are potent mutagens and carcinogens. Metabolites of PAHs can form DNA adducts, considered a necessary step of their carcinogenic property." [PMID:15688365, PMID:21845152]
synonym: "PAH metabolic pathway" EXACT []
is_a: PW:0001229 ! xenobiotic metabolic pathway
created_by: VPetri
creation_date: 2013-07-10T13:58:48Z

[Term]
id: PW:0001439
name: cerium oxide nanoparticle response pathway
def: "A pathway triggered by exposure to cerium oxide nanoparticles, also known as nanoceria. Like other nanoparticles, nanoceria has a broad range of applications. A peculiar feature is the anti-oxidant property; by catalytically reacting with superoxide and hydrogen peroxide, it mimics the activities of superoxide dismutase and catalase enzymes. In addition, beneficial effects on cell differentiation and dopamine production have been shown. However, toxic effects have also been demonstrated." [PMID:19802857, PMID:21369578, PMID:23416263, PMID:23661146]
is_a: PW:0001435 ! nanomaterial response pathway
created_by: VPetri
creation_date: 2013-07-12T10:55:42Z

[Term]
id: PW:0001440
name: arthritis disease pathway
def: "Arthritis collectively describes several conditions whose primary feature is represented by joint pain resulting from inflammation." [wikipedia:http\://en.wikipedia.org/wiki/Arthritis]
is_a: PW:0001018 ! immune disease pathway
created_by: VPetri
creation_date: 2013-07-12T11:28:49Z

[Term]
id: PW:0001441
name: gout disease pathway
is_a: PW:0001440 ! arthritis disease pathway
created_by: VPetri
creation_date: 2013-07-12T11:32:52Z

[Term]
id: PW:0001442
name: inflammatory bowel disease pathway
def: "The inflammatory bowel disease (IBD) results from the deregulation of the immune system to which both genetic and environmental factors contribute. Alterations in pattern recognition receptor signaling, such as Toll-like or Nod and signaling downstream of them, among others, may contribute to and/or lead to the chronic inflammation characteristic of the condition. The main forms of IBD are Crohn's and ulcerative colitis." [PMID:20001899]
synonym: "IBD disease pathway" EXACT []
synonym: "KEGG:05321" RELATED []
is_a: PW:0001018 ! immune disease pathway
created_by: VPetri
creation_date: 2013-07-24T11:11:48Z

[Term]
id: PW:0001443
name: ezetimibe drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of ezetimibe - a drug used to lower the plasma cholesterol level. Ezetimibe is a selective cholesterol absorption inhibitor used both as monotherapy and in combination with statins. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:22910633]
synonym: "Zetia drug pathway" RELATED []
is_a: PW:0000920 ! cardiovascular system drug pathway
created_by: VPetri
creation_date: 2013-08-26T09:32:29Z

[Term]
id: PW:0001444
name: ezetimibe pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of ezetimibe, a selective inhibitor of cholesterol absorption. Genetic variations can result in changes in the availability of the drug." [PMID:22910633]
synonym: "Zetia pharmacokinetics pathway" RELATED []
is_a: PW:0001443 ! ezetimibe drug pathway
created_by: VPetri
creation_date: 2013-08-26T09:33:54Z

[Term]
id: PW:0001445
name: ezetimibe pharmacodynamics pathway
def: "The pathway of ezetimibe-target interaction and of the biochemical or physiological responses to it. Ezetimibe is a selective inhibitor of cholesterol absorption used both as monotherapy and in combination with statins. Genetic variations can cause differences in the response of the organism to the drug." [PMID:22910633]
synonym: "Zetia pharmacodynamics pathway" RELATED []
is_a: PW:0001443 ! ezetimibe drug pathway
created_by: VPetri
creation_date: 2013-08-26T09:34:53Z

[Term]
id: PW:0001446
name: lomitapide drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of lomitapide, a drug used to lower cholesterol levels. Lomitapide is an inhibitor of microsomal triglyceride transfer protein used both as monotherapy and in combination with statins. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:21846156]
is_a: PW:0000920 ! cardiovascular system drug pathway
created_by: VPetri
creation_date: 2013-08-26T09:40:28Z

[Term]
id: PW:0001447
name: lomitapide pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of lomitapide, an inhibitor of microsomal triglyceride transfer protein. Genetic variations can result in changes in the availability of the drug." [PMID:21846156]
is_a: PW:0001446 ! lomitapide drug pathway
created_by: VPetri
creation_date: 2013-08-26T09:41:08Z

[Term]
id: PW:0001448
name: lomitapide pharmacodynamics pathway
def: "The pathway of lomitapide-target interaction and of the biochemical or physiological responses to it. The drug is an inhibitor of microsomal triglyceride transport protein and used to lower cholesterol levels. Genetic variations can cause differences in the response of the organism to the drug." [PMID:21846156]
is_a: PW:0001446 ! lomitapide drug pathway
created_by: VPetri
creation_date: 2013-08-26T09:41:48Z

[Term]
id: PW:0001449
name: nicotine pharmacokinetics pathway
is_a: PW:0000721 ! nicotine pathway
created_by: VPetri
creation_date: 2013-08-28T13:57:46Z

[Term]
id: PW:0001450
name: nicotine pharmacodynamics pathway
is_a: PW:0000721 ! nicotine pathway
created_by: VPetri
creation_date: 2013-08-28T13:58:07Z

[Term]
id: PW:0001451
name: valproic acid drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of valproic acid, a branched short-chain fatty acid derived from valeric acid used as a mood-stabilizing drug and in the treatment of epilepsy. More recently it has also been found to inhibit the proliferation of cancers. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:22668241, PMID:23407051, Wikipedia:http\://en.wikipedia.org/wiki/Valproic_acid]
synonym: "valproate drug pathway" RELATED []
is_a: PW:0000923 ! nervous system drug pathway
created_by: VPetri
creation_date: 2013-08-28T14:01:08Z

[Term]
id: PW:0001452
name: valproic acid pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of valproic acid, a drug used as a mood-stabilizing and for the treatment of epilepsy. Genetic variations can result in changes in the availability of the drug." [PMID:23407051]
synonym: "valproate pharmacokinetics pathway" RELATED []
is_a: PW:0001451 ! valproic acid drug pathway
created_by: VPetri
creation_date: 2013-08-28T14:04:55Z

[Term]
id: PW:0001453
name: valproic acid pharmacodynamics pathway
def: "The pathway of valproic acid-target interaction and of the biochemical or physiological responses to drug. Valproic acid is used as a mood-stabilizing drug and in the treatment of epilepsy. More recently it has also been found to inhibit the proliferation of cancers. Genetic variations can cause differences in the response of the organism to the drug." [PMID:23407051]
synonym: "valproate pharmacodynamics pathway" RELATED []
is_a: PW:0001451 ! valproic acid drug pathway
created_by: VPetri
creation_date: 2013-08-28T14:05:32Z

[Term]
id: PW:0001454
name: Gaucher disease pathway
is_a: PW:0001414 ! brain disease pathway
created_by: VPetri
creation_date: 2013-08-28T14:20:47Z

[Term]
id: PW:0001455
name: doxorubicin drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of doxorubicin." [PMID:21048526]
is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway
created_by: VPetri
creation_date: 2013-08-29T15:06:28Z

[Term]
id: PW:0001456
name: nystatin drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of nystatin - a polyene antifungal drug used to treat yeast infections. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [wikipedia:http\://en.wikipedia.org/wiki/Nystatin]
is_a: PW:0001202 ! genito-urinary system and sex hormones drug pathway
created_by: VPetri
creation_date: 2013-09-05T17:25:49Z

[Term]
id: PW:0001457
name: nystatin pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination -of nystatin. Nystatin is an antifungal that binds to ergosterol - a component of the fungal cell membrane, and also with cholesterol. Genetic variations can result in changes in the availability of the drug." [PMID:16890501, PMID:21482707]
is_a: PW:0001456 ! nystatin drug pathway
created_by: VPetri
creation_date: 2013-09-05T17:29:29Z

[Term]
id: PW:0001458
name: nystatin pharmacodynamics pathway
def: "The pathway of nystatin-target interactions and of the biochemical or physiological responses to drug. Nystatin interacts with both the fungal ergosterol and the host cholesterol but its afinity for ergosterol is higher. The interaction with cholesterol impacts on the uptake and activity of the anti-angiogenic endostatin." [PMID:10991881, PMID:21482707]
is_a: PW:0001456 ! nystatin drug pathway
created_by: VPetri
creation_date: 2013-09-05T17:29:50Z

[Term]
id: PW:0001459
name: amphotericin B drug pathway
is_a: PW:0001202 ! genito-urinary system and sex hormones drug pathway
created_by: VPetri
creation_date: 2013-09-05T17:30:56Z

[Term]
id: PW:0001460
name: amphotericin B pharmacokinetics pathway
is_a: PW:0001459 ! amphotericin B drug pathway
created_by: VPetri
creation_date: 2013-09-05T17:31:28Z

[Term]
id: PW:0001461
name: amphotericin B pharmacodynamics pathway
is_a: PW:0001459 ! amphotericin B drug pathway
created_by: VPetri
creation_date: 2013-09-05T17:31:50Z

[Term]
id: PW:0001462
name: losartan drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of losartan, an angiotensin II receptor type 1 antagonist used in the treatment of hypertension and heart failure. Losartan is one of several angiotensin II receptor type 1 antagonists and the first used on the market. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:21417956, PMID:23487168]
is_a: PW:0000920 ! cardiovascular system drug pathway
created_by: VPetri
creation_date: 2013-09-20T15:43:56Z

[Term]
id: PW:0001463
name: losartan pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of losartan. The drug is an angiotensin II receptor type 1 antagonist used in the treatment of hypertension and heart failure. Genetic variations can result in changes in the availability of the drug." [PMID:21417956]
is_a: PW:0001462 ! losartan drug pathway
created_by: VPetri
creation_date: 2013-09-20T15:47:44Z

[Term]
id: PW:0001464
name: losartan pharmacodynamics pathway
def: "The pathway of losartan-target interaction and of the biochemical or physiological responses to them. Losartan is an angiotensin II receptor type 1 antagonist used in the treatment of hypertension and heart failure. Genetic variations can cause differences in the response of the organism to the drug." [PMID:23487168]
is_a: PW:0001462 ! losartan drug pathway
created_by: VPetri
creation_date: 2013-09-20T15:48:11Z

[Term]
id: PW:0001465
name: warfarin drug pathway
def: "The pharmacokinetics and pharmacodynamics pathway of warfarin, an anticoagulant drug. WArfarin is an effective antagonist of vitamin K dependent clotting. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PMID:23482597]
is_a: PW:0000920 ! cardiovascular system drug pathway
created_by: VPetri
creation_date: 2013-09-20T16:10:07Z

[Term]
id: PW:0001466
name: warfarin pharmacokinetics pathway
def: "The pathway of processing - absorption, distribution, metabolism or elimination - of warfarin." []
is_a: PW:0001465 ! warfarin drug pathway
created_by: VPetri
creation_date: 2013-09-20T16:14:00Z

[Term]
id: PW:0001467
name: warfarin pharmacodynamics pathway
def: "The pathway of warfarin-target interaction and of the biochemical or physiological responses to them." []
is_a: PW:0001465 ! warfarin drug pathway
created_by: VPetri
creation_date: 2013-09-20T16:14:24Z

[Typedef]
id: part_of
name: part_pf