From 75a0ffd1489b873e75e509f00ca09ef7f0880099 Mon Sep 17 00:00:00 2001
From: NishiPhalke <nishaphalke@gmail.com>
Date: Fri, 1 Nov 2024 10:57:17 -0400
Subject: [PATCH] gene exp query changes

---
 .../src/app/applets/gene-expression/const.ts  | 390 ------------------
 .../app/applets/gene-expression/queries.ts    |   4 +-
 .../search/_ccredetails/geneexpression.tsx    |   4 +-
 3 files changed, 3 insertions(+), 395 deletions(-)

diff --git a/screen2.0/src/app/applets/gene-expression/const.ts b/screen2.0/src/app/applets/gene-expression/const.ts
index 7cef0dc0..c5b9bae7 100644
--- a/screen2.0/src/app/applets/gene-expression/const.ts
+++ b/screen2.0/src/app/applets/gene-expression/const.ts
@@ -1,392 +1,2 @@
-
-export const MOUSE_GENE_EXP = ["ENCSR000AJV",
-"ENCSR004XCU",
-"ENCSR017JEG",
-"ENCSR020DGG",
-"ENCSR039ADS",
-"ENCSR049UJU",
-"ENCSR062VTB",
-"ENCSR080EVZ",
-"ENCSR095VGF",
-"ENCSR096STK",
-"ENCSR115TWD",
-"ENCSR150CUE",
-"ENCSR160IIN",
-"ENCSR173PJN",
-"ENCSR178GUS",
-"ENCSR185LWM",
-"ENCSR216NEG",
-"ENCSR284AMY",
-"ENCSR284YKY",
-"ENCSR285WZV",
-"ENCSR304RDL",
-"ENCSR307BCA",
-"ENCSR331XCE",
-"ENCSR337FYI",
-"ENCSR343YLB",
-"ENCSR347SQR",
-"ENCSR362AIZ",
-"ENCSR367ZPZ",
-"ENCSR370SFB",
-"ENCSR401BSG",
-"ENCSR420QTO",
-"ENCSR438XCG",
-"ENCSR442XRH",
-"ENCSR448MXQ",
-"ENCSR457RRW",
-"ENCSR465PBJ",
-"ENCSR466KZY",
-"ENCSR508GWZ",
-"ENCSR526SEX",
-"ENCSR537GNQ",
-"ENCSR538WYL",
-"ENCSR541XZK",
-"ENCSR557RMA",
-"ENCSR559TRB",
-"ENCSR597UZW",
-"ENCSR611PTP",
-"ENCSR636CWO",
-"ENCSR647QBV",
-"ENCSR648YEP",
-"ENCSR691OPQ",
-"ENCSR712PLG",
-"ENCSR719NAJ",
-"ENCSR727FHP",
-"ENCSR748DUR",
-"ENCSR750YSX",
-"ENCSR752RGN",
-"ENCSR760TOE",
-"ENCSR764OPZ",
-"ENCSR792RJV",
-"ENCSR795WFC",
-"ENCSR809VYL",
-"ENCSR823VEE",
-"ENCSR826HIQ",
-"ENCSR830IVQ",
-"ENCSR848GST",
-"ENCSR848HOX",
-"ENCSR851HEC",
-"ENCSR867YNV",
-"ENCSR906YQZ",
-"ENCSR908JWT",
-"ENCSR921PRX",
-"ENCSR932TRU",
-"ENCSR943LKA",
-"ENCSR968QHO",
-"ENCSR970EWM",
-"ENCSR982MRY",
-"ENCSR992WBR",
-"ENCSR996TVY"]
-
-export const HUMAN_GENE_EXP = ["ENCSR828TEI",
-"ENCSR919QJT",
-"ENCSR314LXG",
-"ENCSR429EWK",
-"ENCSR584JXD",
-"ENCSR196KBV",
-"ENCSR551NII",
-"ENCSR991HIR",
-"ENCSR964JRR",
-"ENCSR858QEL",
-"ENCSR880EGO",
-"ENCSR504NIU",
-"ENCSR648OSR",
-"ENCSR406SAW",
-"ENCSR313COD",
-"ENCSR719PXC",
-"ENCSR740YMS",
-"ENCSR528ZKN",
-"ENCSR244ISQ",
-"ENCSR052FJA",
-"ENCSR571RXE",
-"ENCSR080HPT",
-"ENCSR908ZAS",
-"ENCSR796HLX",
-"ENCSR158KFO",
-"ENCSR839ZDH",
-"ENCSR692DIM",
-"ENCSR971GPJ",
-"ENCSR136WGP",
-"ENCSR446LDS",
-"ENCSR444WHQ",
-"ENCSR568YRP",
-"ENCSR233IJT",
-"ENCSR332DBS",
-"ENCSR320BRR",
-"ENCSR336VTK",
-"ENCSR130TZW",
-"ENCSR735JKB",
-"ENCSR015PUN",
-"ENCSR559HWG",
-"ENCSR841QAC",
-"ENCSR306IAW",
-"ENCSR797BPP",
-"ENCSR343XXH",
-"ENCSR818DBU",
-"ENCSR931ATS",
-"ENCSR231ICM",
-"ENCSR113CCF",
-"ENCSR889IAP",
-"ENCSR870IUI",
-"ENCSR854VRX",
-"ENCSR267FRL",
-"ENCSR568UGZ",
-"ENCSR485WBR",
-"ENCSR729VMM",
-"ENCSR712BRU",
-"ENCSR945VLG",
-"ENCSR035SKV",
-"ENCSR761SHI",
-"ENCSR094RQC",
-"ENCSR800KLD",
-"ENCSR450BNZ",
-"ENCSR828JSJ",
-"ENCSR294AKN",
-"ENCSR108MAU",
-"ENCSR580GSX",
-"ENCSR653DFZ",
-"ENCSR669KQU",
-"ENCSR535VTR",
-"ENCSR894WMQ",
-"ENCSR379YAE",
-"ENCSR895ZTB",
-"ENCSR245ATJ",
-"ENCSR802HPM",
-"ENCSR257NIR",
-"ENCSR480SLD",
-"ENCSR645TCG",
-"ENCSR460YCS",
-"ENCSR321PGV",
-"ENCSR151NGC",
-"ENCSR774MGO",
-"ENCSR129VBC",
-"ENCSR631FXT",
-"ENCSR425RGZ",
-"ENCSR411MUF",
-"ENCSR355JZC",
-"ENCSR381OTM",
-"ENCSR201XOZ",
-"ENCSR398REC",
-"ENCSR589EBT",
-"ENCSR674KHG",
-"ENCSR759TPN",
-"ENCSR391VGU",
-"ENCSR701TST",
-"ENCSR410MSS",
-"ENCSR826FNO",
-"ENCSR003BTD",
-"ENCSR029KNZ",
-"ENCSR853WOM",
-"ENCSR379DEC",
-"ENCSR420ZKB",
-"ENCSR532LJV",
-"ENCSR229LFK",
-"ENCSR825UXP",
-"ENCSR797RXV",
-"ENCSR763OMY",
-"ENCSR019ICB",
-"ENCSR276MMH",
-"ENCSR146ZLV",
-"ENCSR687HJY",
-"ENCSR842NDO",
-"ENCSR609NZM",
-"ENCSR357BYU",
-"ENCSR151FXS",
-"ENCSR745APD",
-"ENCSR266PVZ",
-"ENCSR841ADZ",
-"ENCSR648YUM",
-"ENCSR140DCD",
-"ENCSR853TXT",
-"ENCSR429EGC",
-"ENCSR094VRQ",
-"ENCSR420YFF",
-"ENCSR857WJK",
-"ENCSR447WLU",
-"ENCSR827IXS",
-"ENCSR942YMN",
-"ENCSR652PHZ",
-"ENCSR132VGJ",
-"ENCSR352JCY",
-"ENCSR892LBU",
-"ENCSR619DQO",
-"ENCSR441IDG",
-"ENCSR278TQR",
-"ENCSR790BBE",
-"ENCSR146ZSP",
-"ENCSR897JEH",
-"ENCSR678TMV",
-"ENCSR676SRP",
-"ENCSR135IAL",
-"ENCSR621PZI",
-"ENCSR469WPG",
-"ENCSR876TAN",
-"ENCSR001HHK",
-"ENCSR045GTF",
-"ENCSR967JPI",
-"ENCSR903XMI",
-"ENCSR586SYA",
-"ENCSR438YPF",
-"ENCSR712GOC",
-"ENCSR801MKV",
-"ENCSR997KDB",
-"ENCSR403SZN",
-"ENCSR194HVU",
-"ENCSR838XNO",
-"ENCSR800WIY",
-"ENCSR344MQK",
-"ENCSR501DTN",
-"ENCSR911XSA",
-"ENCSR113HQM",
-"ENCSR275SNI",
-"ENCSR629HFE",
-"ENCSR320OTJ",
-"ENCSR434TEU",
-"ENCSR816HLU",
-"ENCSR098BUF",
-"ENCSR579KTN",
-"ENCSR244HHV",
-"ENCSR436QDU",
-"ENCSR985WSV",
-"ENCSR944UJZ",
-"ENCSR061HMO",
-"ENCSR291TRJ",
-"ENCSR365ARV",
-"ENCSR165QTZ",
-"ENCSR954PZB",
-"ENCSR882HXI",
-"ENCSR622PIH",
-"ENCSR111PSY",
-"ENCSR042GYH",
-"ENCSR252UHW",
-"ENCSR071DYD",
-"ENCSR450EXF",
-"ENCSR377MTB",
-"ENCSR968WKR",
-"ENCSR729CAZ",
-"ENCSR457ENP",
-"ENCSR272UNO",
-"ENCSR096UGR",
-"ENCSR131FDP",
-"ENCSR727DPU",
-"ENCSR075ZTG",
-"ENCSR544SAU",
-"ENCSR450ENK",
-"ENCSR653ZJF",
-"ENCSR558SEE",
-"ENCSR330UMQ",
-"ENCSR630VJN",
-"ENCSR226KML",
-"ENCSR563VMC",
-"ENCSR837VMK",
-"ENCSR584CVV",
-"ENCSR023ZXN",
-"ENCSR523RGW",
-"ENCSR464VSR",
-"ENCSR052LON",
-"ENCSR792OIJ",
-"ENCSR474TRG",
-"ENCSR420NLC",
-"ENCSR620LQN",
-"ENCSR033XWU",
-"ENCSR853BNH",
-"ENCSR185TQB",
-"ENCSR900FUP",
-"ENCSR516TTH",
-"ENCSR317HKT",
-"ENCSR368HRJ",
-"ENCSR927KSI",
-"ENCSR495HDM",
-"ENCSR516BJM",
-"ENCSR010HIU",
-"ENCSR924MSZ",
-"ENCSR395DKP",
-"ENCSR812AKX",
-"ENCSR837ZLY",
-"ENCSR862RGX",
-"ENCSR510MIA",
-"ENCSR863EIY",
-"ENCSR413QAL",
-"ENCSR755FNG",
-"ENCSR648KDM",
-"ENCSR733JBX",
-"ENCSR288RRZ",
-"ENCSR290IHM",
-"ENCSR168PXI",
-"ENCSR504QMK",
-"ENCSR096LTX",
-"ENCSR900SGE",
-"ENCSR896YYL",
-"ENCSR615EEK",
-"ENCSR074FTH",
-"ENCSR238ZZD",
-"ENCSR863VFU",
-"ENCSR377FPC",
-"ENCSR198QAJ",
-"ENCSR177XCG",
-"ENCSR071ZLM",
-"ENCSR563SJY",
-"ENCSR718RTN",
-"ENCSR394ZSF",
-"ENCSR479MNN",
-"ENCSR128CYL",
-"ENCSR585EUI",
-"ENCSR146LBD",
-"ENCSR698RPL",
-"ENCSR106SZN",
-"ENCSR351OTL",
-"ENCSR258ELN",
-"ENCSR631NUQ",
-"ENCSR899OKE",
-"ENCSR432EBE",
-"ENCSR394HJK",
-"ENCSR448BTT",
-"ENCSR500JSJ",
-"ENCSR773COB",
-"ENCSR073XFZ",
-"ENCSR820PHH",
-"ENCSR636LEU",
-"ENCSR570DQR",
-"ENCSR257FJF",
-"ENCSR146GSS",
-"ENCSR714CHF",
-"ENCSR034DEZ",
-"ENCSR266SBI",
-"ENCSR882RCG",
-"ENCSR681ARR",
-"ENCSR502PAY",
-"ENCSR197GCF",
-"ENCSR534OAS",
-"ENCSR296PMS",
-"ENCSR752UNJ",
-"ENCSR297AZN",
-"ENCSR235PLU",
-"ENCSR816IZA",
-"ENCSR915EBZ",
-"ENCSR562BUN",
-"ENCSR743GKS",
-"ENCSR354QPN",
-"ENCSR000AEL",
-"ENCSR956ZVR",
-"ENCSR184LTL",
-"ENCSR671IYC",
-"ENCSR579BDN",
-"ENCSR202OWR",
-"ENCSR025BZY",
-"ENCSR750ETS",
-"ENCSR078WNY",
-"ENCSR011VQI",
-"ENCSR471RUK",
-"ENCSR323GUF",
-"ENCSR308XAR",
-"ENCSR484WZL",
-"ENCSR182CBU",
-"ENCSR754WLW",
-"ENCSR094GVZ",
-"ENCSR938LSP"
-]
-
-
-
 export const GeneExpressionInfoTooltip =
   "This bar plot displays the expression level of a given gene across available cell types and tissues derived from RNA-seq data. By default, the data displayed is log2(TPM + 0.01), but this may be customized by selecting from the data dropdown; FPKM values are also available and the log scale may be turned off. TPM and RPKM are two metrics of gene expression levels and they differ slightly in their approaches to normalizing for sequencing depth and gene length. The sort order dropdown allows sorting of the data by TPM or FPKM and also allows grouping of the expression values by tissue. Mousing over the bars displays more information about the expriments that produced the data points, and clicking on a bar redirects to the corresponging experiment at the ENCODE portal."
diff --git a/screen2.0/src/app/applets/gene-expression/queries.ts b/screen2.0/src/app/applets/gene-expression/queries.ts
index 1237bb9e..a23b3102 100644
--- a/screen2.0/src/app/applets/gene-expression/queries.ts
+++ b/screen2.0/src/app/applets/gene-expression/queries.ts
@@ -1,7 +1,7 @@
 import { gql } from "@apollo/client"
 export const GENE_EXP_QUERY = gql`
-query geneexpression($assembly: String!, $accessions: [String], $gene_id: [String]) {
-  gene_dataset(accession: $accessions) {
+query geneexpression($assembly: String!, $gene_id: [String]) {
+  gene_dataset(processed_assembly: $assembly) {
     biosample
     tissue
   	cell_compartment
diff --git a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx
index b892e22f..5aaff693 100644
--- a/screen2.0/src/app/search/_ccredetails/geneexpression.tsx
+++ b/screen2.0/src/app/search/_ccredetails/geneexpression.tsx
@@ -6,7 +6,6 @@ import { useQuery } from "@apollo/client"
 import { Button, Typography, Stack, MenuItem, FormControl, SelectChangeEvent, Checkbox, InputLabel, ListItemText, OutlinedInput, Select, ToggleButton, ToggleButtonGroup, FormLabel, Box } from "@mui/material"
 import Grid from "@mui/material/Grid2"
 import Image from "next/image"
-import { HUMAN_GENE_EXP, MOUSE_GENE_EXP } from "../../applets/gene-expression/const"
 import { GENE_EXP_QUERY, GENE_QUERY, GET_ORTHOLOG, GET_ORTHOLOG_DATA, GET_ORTHOLOG_VARS } from "../../applets/gene-expression/queries"
 import { ReadonlyURLSearchParams, usePathname, useSearchParams, useRouter } from "next/navigation"
 import ConfigureGBModal from "./configuregbmodal"
@@ -91,8 +90,7 @@ export function GeneExpression(props: {
   } = useQuery(GENE_EXP_QUERY, {
     variables: {
       assembly: dataAssembly,
-      gene_id: dataGeneID && dataGeneID.gene.length > 0 && dataGeneID.gene[0].id.split(".")[0],
-      accessions: dataAssembly === "GRCh38" ? HUMAN_GENE_EXP : MOUSE_GENE_EXP
+      gene_id: dataGeneID && dataGeneID.gene.length > 0 && dataGeneID.gene[0].id.split(".")[0]      
     },
     skip: !gene || !dataGeneID || (dataGeneID && dataGeneID.gene.length === 0),
     fetchPolicy: "cache-and-network",