Download our data from the below links
Most data was taken from The Cancer Genome Atlas (TCGA) via either the Genome Data Analysis Center at the Broad Institute or cBioPortal.
TCGA RNASeqv2 Expression Data
This file has all of the RNA expression data used for differential gene expression analysis. The relevant script is here. The file is in .RData format. Note that this data belongs to TCGA, but we have merely coerced it into a format compatible with our analyses.
TCGA Clinical Data
This file has all of the clinical annotations for patients in TCGA. The file is referenced by numerous scripts in copy number and methylation analyses. The file is in .RDS format. Note that this data belongs to TCGA, but we have merely coerced it into a format compatible with our analyses.
Human Gene List
This file contains aliases for HUGO identifiers. It can be used in conjunction with the methylation and copy number analyses to narrow the list of genes being investigated.
Lincscloud Input Files
These files have all the inputs to Lincscloud. There are 8 files per cancer. 4 contain Affymetrix IDs, which Lincscloud does not accept but other connectivity map services may. The other 4 contain converted HUGO IDs. There are 2 files per sex, one indicating genes up (i.e., resistance signature) and the other indicating genes down (i.e., sensitivity signature) in tumors. Note that when inputting lists to Lincscloud, the resistance signature ought to be listed under genes down, since you are looking for a perturbagen that down-regulates the resistance signature. All 8 files are contained in folders separated by cancer type.
Head and Neck Squamous Cell Carcinoma (HNSC)
Kidney Chromophobe (KICH)
Kidney Renal Clear Cell Carcinoma (KIRC)
Liver Hepatocellular Carcinoma (LIHC)
Lung Adenocarcinoma (LUAD)
Lung Squamous Cell Carcinoma (LUSC)
Thyroid Carcinoma (THCA)
Pan-Cancer Analyses
Tumor and Normal Expression
These files contain all of the tumor (neoplastic) and normal (nonneoplastic) expression from TCGA. These files are specifically used in the Permutation Analysis. Note that this data belongs to TCGA, but we have merely coerced it into a format compatible with our analyses.
Tumor and Normal Clinical Data
These files contain all of the tumor (neoplastic) and normal (nonneoplastic) clinical data from TCGA. These files are specifically used in the Permutation Analysis. Note that this data belongs to TCGA, but we have merely coerced it into a format compatible with our analyses.