Supplementary Figure 7: Testing for enrichment of amplification and single nucleotide variants in oncogene negative samples

Testing for the enrichment of a) gene amplification and b) SSNVs/Indels in genes for oncogene negative samples. Oncogene negative patients were defined as those having no known driver mutation in the RAS/RAF/receptor tyrosine kinase (RTK) pathway. We created a null distribution of P values using Fisher’s exact test on 100 random gene sets (while controlling for overall connectivity in protein-protein interaction space), which is shown as bar plots. The observed p value of data from Figure 3, main text is indicated as the red line. The P values from the data in Figure 3 are better in 96 of a 100 random sets for the amplifications (P = 0.04). This is not the case for the SSNVs and indels (P = 0.19).