Fig. 2: DMRs functional classification.

Table in (a) reports the number of genes affected by all, hyper-methylated (Hyper) and hypo-methylated (hypo) DMRs. For each patient we also report number of genes with DMRs overlapping 5' regulatory region (Reg, including 1–5 kb from TSS, promoters, first exons and 5'UTRs), gene-body (GB, including internal introns and exons), 3'UTR and enhancers (genes predicted by FANTOM to be regulated by enhancers). The discrepancy between total number of genes (All) and the sum of Reg, GB and 3'UTR is due to the fact that few genes have DMRs in more than one genic element. The barplot of (b) reports the total number of DM genes with DMRs at different genomic elements (5' regulatory region, Reg, internal introns and exons, GB, 3'UTR and enhancers of Fantom Genes). with DMRs in all regions (All, both inside and outside CGIs), inside CpG islands (CGI) and outside CpG islands (NoCGI) at different genomic elements (5' regulatory region, Reg, internal introns and exons, GB, 3'UTR and enhancers of Fantom Genes). Textured bars show the number of DMGs with DMRs in sparse CpG regions (NoCGI). Numbers above bars show the percentage of DMGs in sparse CpG regions. Horizontal brackets above each group of three bars summarize average percentages of the three samples. The barplot of (c) reports the total number of DM-DEGs for the four regulatory categories: over-expressed genes with hyper-methylated DMRs (Hyper-Over), over-expressed genes with hypo-methylated DMRs (Hypo-Over), under-expressed genes with hyper-methylated DMRs (Hyper-Under), under-expressed genes with hypo-methylated DMRs (Hypo-Under). Numbers above each bar show the relative percentage of DM-DEGs with respect to all DM-DEGs for each sample. Horizontal brackets above each group of three bars summarize average percentages within the three samples. The barplot of (d) report the number of hyper- and hypo-methylated DM-DEGs with respect to total number of DMGs in CGIs and sparse CpG regions (NoCGI). Textured bars show the number of DM-DEGs. Numbers above each bar show the percentage of DM-DEGs with respect to DMGs. Horizontal brackets above each group of three bars summarize average percentages within the three samples.