Cancer gene and annotation data
To construct the reported cancer gene database, we used gene sets from the CGC database (released on Dec, 2010) and CGI database (downloaded on Feb, 2011). The cancer pathways for the cancer pathway gene database construction were assigned based on statistical significance from one-tailed Fisher's exact test for overlapping genes between reported cancer gene sets and canonical pathways from public pathway databases, including KEGG (Release 57.0), BioCarta, and Reactome (downloaded on Feb, 2011).
We also created a gene ID database to convert various input identifiers into standard gene symbols with HUGO Gene Nomenclature Committee (HGNC) (downloaded on Feb, 2011) data for the standard gene symbols and with Entrez Gene (downloaded on Feb, 2011) and UniProt (Release 2011_03) data for the gene IDs, protein IDs, and functional annotations.