Connectivity Mapping (cmap) Application

A web server-based application can be found here.

Call application in R

library(shiny)

runGitHub("cmap", "jessicaw9910")

Input file

To use this workflow, enter a CSV file containing 3 columns of data from differential gene expression (DGE) analysis to create a rank ordered list of a given biological condition. An example file is provided in the test.csv file.

1. gene symbol (column 1) - be sure these gene names map to the latest using AnnotationHub()
2. logFC change (column 2) - log₂ fold change relative to reference condition from DGE
3. ranking metric (column 3) - gene-level statistics, such as p-value, adjusted p-value, or absolute t-statistic, from a differential expression test. Note that identical values will force arbitrary ranking so select a metric with minimum number of duplicates. This is frequently an issue if adjusted p-values have been corrected using Benjamini-Hochberg.

data

• LINCS_L1000_Chem_Pert.Rda - contains cleaned Enrichr LINCS L1000 up-regulated and down-regulated gene lists in the form of matrices and lists
• new_moa.csv - contains mapping of drugs to mechanisms of action from clue.io, L1000 FWD, chemical supplier website (e.g., Tocris, Sigma Aldrich), and literature