Fig. 3

Results of the application of OncodriveFML to identify driver promoters and 5′ UTRs. The results of OncodriveFML are illustrated on mutations found across the pan-cancer cohort (a–d) and the cohorts of lower grade gliomas (e, f) and bladder urothelial carcinomas (g–i) of the WG-505 dataset. a, e, g QQ plots comparing the expected and observed distribution of FM bias p values of promoters and 5′ UTRs mutated in the respective cohorts. b–d, h Mutation needle-plots of selected promoters and 5′ UTRs, with a zoom at mutations located in the proximity of the transcription start site (TSS), or the 5 bps of the 5′ UTR closer to the CDS, respectively. f Comparison of the expression of two genes with significantly FM biased promoters in the cohort of lower grade gliomas in samples with mutations in the promoter and unmutated samples. In the boxplots the gene expressions of the mutated samples (on the left) is compared to those of unmutated samples (on the right). The expression values are reported in RPKM (Reads Per Kilobase of transcript per Million mapped reads) on the y-axis and the number of samples (mutated and normal) in each set are indicated with dots on the boxplots. The significance of the differential expression between mutated and non-mutated samples is reported at the top of each plot (Wilcoxon rank-sum test). I. Significance of the 5′ UTR of the TBC1D12 gene across several cohorts of both the WG-505 and WG-608 datasets