Stanford - Cancer Genome Atlas Analysis of Colorectal Cancer

Gene Selection

  1. COSMIC cancer genes: to date, 484 genes were defined as cancer genes according to Catalogue of Somatic Mutations in Cancer (COSMIC). The list of genes, cancer_gene_ census.tsv, was downloaded from their website export/
  2. TCGA cancer genes: we added the list of genes that associated with tumor aggressiveness in TCGA colorectal cancer paper
    1. Significantly mutated genes: top 13 mutated genes in hypermutated samples and top 19 mutated genes in non-hypermutated samples from TCGA supplementary table 3
    2. Copy number changed genes: the genes in peak (by supplementary table4) of significant focal amplication/deletion from TCGA supplementary table 11
    3. Expression signatures: top 30 genes that have expression signature associate with tumor aggressiveness (TCGA Figure 5b)
    4. Methylation signatures: top 344 genes with prove that has the highest compound p values (TCGA supplementary table 11)
  3. 20 known target genes for microsatellite Instability: Our supplementary table 1 shows the list of 20 genes including TGFBR2 and ACVR2A.
Collectively 1,085 genes were included in our study.