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Fig. 4 | Genome Biology

Fig. 4

From: Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

Fig. 4

Significantly mutated, rearranged, and differentially methylated coding and non-coding regions. a QQ plots for significantly mutated coding sequence (CDS), promoters, and enhancers using FSig-SNV. b QQ plots for significantly rearranged CDS, promoters, and enhancers using FSig-SV. c DNA methylation changes and their association with gene expression. Left and middle: Significantly differentially methylated promoters and enhancers. Violin plots show a significant difference in methylation levels (Wilcoxon test p value < 0.05) at hyper- and hypo-methylated cis-regulatory regions (promoters and enhancers) between 333 tumor and 35 normal samples. Right: Scatter plots show examples of genes differentially expressed due to a hyper-methylated promoter (PROM1) and a hypo-methylated enhancer (MTBP) in tumor vs. normal samples. MTBP and PROM1 have been reported to be differentially expressed in TMPRSS2:ERG positive prostate tumors [122]. A significant decrease in PROM1 expression in 152 TMPRSS2:ERG fusion positive TCGA samples (red) vs. normal (pink) is associated with a hyper-methylated promoter (cg04203238). A significant increase in MTBP expression in ERG fusion positive samples (yellow) is associated with hypo-methylation in an enhancer (cg11476306). CDS coding sequence

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