Input types
Available input types include a list of gene symbols, Entrez gene IDs, or UniProt accessions and output files from prediction tools, such as Sorting Intolerant From Tolerant (SIFT) [10] and PolyPhen [11], which evaluate functional effects of mutations on proteins. CaGe parses the output of those tools to extract the list of genes that have somatic mutations evaluated as functionally damaging, classify them into previously reported and novel candidate cancer genes, and conduct pathway analyses to give insights into underlying carcinogenic mechanisms. Thus, CaGe offers straightforward data processing from HGT-based data without additional data conversion.