Fig. 4: Gene-centric mutation rate aggregated across the collection of REs associated to a gene (CREAG).
From: Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer
a QQ-plot that shows the expected (x-axis) and observed (y-axis) significance values of mutational burden for all CREAGs. b Super-enhancer associated genes that have somatic SNVs. c Manhattan plot showing the genomic location (x-axis) and significance (y-axis) of mutational burden for all CREAGs. d Enrichment of super-enhancer associated genes in FM CREAGs (dark green) vs. random selection (light green) (PGSEA = 0.01). e Volcano plot showing the fold change of median gene expression (x-axis) and the significance value (y-axis) of the putative target gene in samples with single nucleotide variants in a CREAG vs. wild-type samples. The histogram on top of the scatterplot shows more overexpression events (−log2(FC) > 0) in the presence of single nucleotide variants than under expression events (−log2(FC) < 0). f HGSOC (n = 169) non-coding oncoplot showing the top 10 ranking genes in terms of number of samples with mutations overlapping its CREAG. g PAX8 locus showing the mutations within the PAX8 CREAG. h The number of samples with mutations overlapping the PAX8 CREAG are statistically significant in Skin-Melanoma, Ovary-Adeno-CA and Kidney-RCC datasets. i HGSOC (n = 110) oncoplot with PAX8 copy number variation, PAX8 CREAG mutation, TEAD4 and PAX8-binding site mutations.
