Fig. 3

(A) A large overlap is seen in the differentially methylated CpGs in SETD2 cases and VHL mutants in renal cancer. (B) Comparing SETD2 cases to pan-negative (VHL, PBRM1, and BAP1 negative) WT samples removes the confounding effect and finds 1664 differentially methylated CpGs, clustered using complete-linkage clustering and distance measure given by euclidean distance. (C) Genomic distribution of differentially methylated CpG sites shows that hypomethylated CpGs are strongly enriched in the gene bodies whereas hypermethylated CpGs show a more wide-spread distribution. Illumina array shows the distribution in the entire 450k methylation array; 3’UTR: 3’ untranslated region, 5’UTR: 5’ untranslated region; TSS1500: 1500 bp upstream of transcription start site, TSS200: 200 bp upstream of transcription start site (D) Gene enrichment analysis of differentially methylated sites. A large number of significantly enriched processes are involved in developmental pathways. The gene ratio refers to the number of genes in that gene set annotated to the GO term divided by the total number of genes in the gene set. A higher gene ratio implies greater overrepresentation of genes to the particular GO term.