Figure 5

AzaC-induced changes in gene expression are not linked to gross hypomethylation of CpG islands. (a) Smoothed percentage methylation plot of the DAZL promoter region, showing individual CpGs (dots) and smoothed methylation (lines) for untreated (red) and treated (blue). (b) Overlap between genes with a methylated CpG island overlapping TSS (mCpG > 80%) and upregulated genes (BH-fdr <0.05). (c) Reference CpGs are placed into integer bins (in the range of 0 to 100) corresponding to AzaC untreated% methylation. The mean difference in methylation is calculated for the CpGs in each bin, and plotted. (d) Scatter plot of difference in expression versus difference in CpG island methylation at genes with a CpG island within 10 kb of the TSS, showing all genes (blue) and significantly regulated genes (red). (e) Scatter plot of difference in expression versus difference in CpG island shore methylation at genes with a CpG island within 10 kb of the TSS, showing all genes (blue) and significantly regulated genes (red). (f) Histogram of relative methylation differences for upregulated and all genes. The relative difference in the promoter (+/- 2 kb TSS) methylation for significant upregulated (red) and all genes (blue) is calculated and the distribution is plotted.