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. 2013 Sep 19;42(1):109–127. doi: 10.1093/nar/gkt838

Figure 3.

Figure 3.

Density distribution of differential DNA methylation as function of distance from TSS. The distance is represented on a log scale. For each bin, the normalized density of sites was calculated as [(number of DM sites per bin)/(total number of DM sites)]/[(number of sites in the filtered HM450K array per bin)/(total number of sites in the filtered HM450K array)]. For both the NUM sites (shown as filled circles) and the GUM sites (shown as open circles), the normalized density of the DM sites was <1 at a distance of <1000 bp from TSS, and was >1 at a distance of >1000 bp from TSS, suggesting that the DM sites were depleted in the promoters but enriched within distal regulatory elements. More GUM than NUM sites resided proximal to TSS. Arrow indicates an enrichment of the NUM sites outside promoter regions (∼1000–4000 bp from TSS), which was largely explained by the overrepresentation of the NUM sites in CpG-island shores (Supplementary Figure S8). Sites with nonsignificantly changed methylation (NS) are shown as open squares.