Figure 2. DNA methylation and its relationship with gene expression.
a, The mean Spearman correlation coefficient at various distances between the methylation level of autosomal DMRs and the expression of the nearest gene. These correlations are shown for DMRs: overlapping genes (Genebody), overlapping enhancers (Enhancer), overlapping promoters or CpG islands (CGIs) or CGI shores (Promoter, CGI, CGI shore), not overlapping genes (Intergenic) and all remaining DMRs (Undefined). b, Heatmap showing each motif’s tissue-specific methylation preference. The tissues are colored according to Fig 1c., and the ordering is listed at the bottom of the figure. The bar plot at the end of the panel shows the number of times the motif was present in the 20 motif models. c, The number of base pairs covered by PMDs in all samples. d, The distribution of expression inside and outside of PA-2 PMDs across various samples. Notches indicate a confidence interval estimated from 1,000 bootstrap samples. Each PMD boxplot consists of 3,627 genes and each non-PMD boxplot consists of 22,907 genes. e-f, Histone modification profiles in and around PMDs in PA-2 (e) and IMR90 (f).