Fig. 4

Heatmaps showing the association between the location of hypermethylated (a) and hypomethylated (b) CpG sites and enriched regions for several chromatin marks and cell lines. Chromatin marks peak location information for each cell line was extracted from the ENCODE BROAD Histone project information available at the UCSC Genome Browser. Associations between CpG site and chromatin mark peak locations were tested using a Fisher's exact test. P values were adjusted for multiple comparisons and only those falling under a 0.05 FDR threshold are shown as colored spots in the heatmap. The base-2 logarithm of the odds ratio (OR) was used as a measure of effect size. Associations with higher effect sizes are drawn in darker shades of red. There are statistically significant associations of hypermethylated (a) CpGs with the repressive histone mark H3K27me3 and the polycomb group protein EZH2 in most differentiated ENCODE cell lines. On the other hand, hypomethylated probes are associated with regions enriched in H3K4me1 (b)