Additional file 3 of Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer

Additional file 3. Table S1 Synonymous candidates v.s. Non-synonymous Drivers(PCAWG) mutual exclusivity analysis: Columns are cohort tested, synonymous candidate gene, PCAWG driver gene, number of patients have mutations in both genes, number of patients only have mutations in synonymous candidate gene, number of patients only have mutations in PCAWG driver gene, number of patients don’t have mutations in either of the genes, Fisher’s exact test statistics(odds ratio), Fisher’s exact test p-value(left-tail), Benjamini-Hochberg corrected q value. Table S2: Non-synonymous Drivers(PCAWG) vs. Non-synonymous Drivers(PCAWG) mutual exclusivity analysis: Columns are cohort tested, first PCAWG driver gene, second PCAWG driver gene, number of patients have mutations in both genes, number of patients only have mutations in first PCAWG driver gene, number of patients only have mutations in second PCAWG driver gene, number of patients don’t have mutations in either of the genes, Fisher’s exact test statistics(odds ratio), Fisher’s exact test p-value(left-tail), Benjamini-Hochberg corrected q value. Table S3: Synonymous candidates vs. Non-synonymous Drivers(PCAWG) co-occurrence analysis: Columns are cohort tested, synonymous candidate gene, PCAWG driver gene, number of patients have mutations in both genes, number of patients only have mutations in a synonymous candidate gene, number of patients only have mutations in PCAWG driver gene, number of patients don’t have mutations in either of the genes, Fisher’s exact test statistics (odds ratio), Fisher’s exact test p-value(right-tail), Benjamini-Hochberg corrected q value. Table S4: Cander drivers identified in Tokheim et al. using different algorithms: Columns A-I are driver genes detected by Tokheim et al. with different algorithms. Column J is candidate genes identified by MutSigCVsyn. For each column, genes that are overlapped with MutSigCVsyn candidates are highlighted in red. Table S5: BCL2 synonymous mutations in PCAWG & overlap with synMICdb. Table S6: gProfiler analysis on MutSigCVsyn candidate genes: output of gProfiler analysis result using all synonymous candidate genes. Table S7: Synonymous candidate genes and FDR q values identified by MutSigCVsyn in PCAWG: Detailed q-value data for figure 3C heatmap.