Target Selection

Gene Selection

  1. COSMIC cancer genes: As of February 2015, COSMIC database listed 538 genes as cancer genes that have been implicated in cancer development from the scientific literature. The list of genes, cancer_gene_census.tsv, was downloaded from their website
  2. Genes from TCGA studies: we included genes with significant mutations or within focal amplifications/deletions according to Broad Firehose analysis (2015_04_02 version).
    1. Significantly mutated genes: Broad Firehose used MutSig 2CV. Total 676 genes had significant mutations from 25 cancer types with false discovery rate < 0.001
    2. Genes in significant focal copy number change: Broad Firehose used GISTIC 2.0. Total 1,163 genes were in focal deletion while 373 genes were in focal amplification.

Collectively 2,180 genes genes were included in our study.

miR Selection

We included all 1,751 miR in miR-Sequencing data from 25 cancers

Protein selection

We included all 228 proteins in RPPA data from 25 cancers