The ‘proprietary selection’ of cancer genes refers to the list of 98 genes, after filtering of the genes from the public domain. The aim of the filtering was to generate a list of genes with reported relevance in the cancer field, so to exclude genes that may not be relevant for cancer after all. Non-coding mutations have been filtered out (e.g. silent mutations) and only mutations that have been reported in cancer patients were kept. In addition, relevant copy number variations are included in the analysis.
The subset of 38 ‘commonly occurring and well known genes’ are a subset of the 98 genes. It contains the 35 most frequently mutated, amplified or deleted genes (TP53, CDKN2A, KRAS etc.) + 3 well known genes that everybody would miss if they are not included (BRCA2, SMAD4, and the BCR-ABL translocation). The ANOVA analysis is restricted to 38 genes for statistical reasons (due to the number of cell lines).