Fig. 5: Correlation of DNA methylation, nucleosome positioning and gene expression.

a Methylation probability (shaded area) and nucleosome coverage (solid lines) around genes with expression in the top 10% (blue) or bottom 10% (red) expression level. b Log2 of the fold change in expression for genes with highly and lowly methylated promoters. c Gene expression difference between methylated and not methylated samples. RNA level difference is plotted on the x-axis and the Adj. p value on the y-axis. Downregulated (20 genes) and upregulated (63 genes) genes are shown in red and green, respectively. The genes with the highest changes are highlighted. d Promoter motif enrichment for genes with highly methylated promoters and increase in expression level using HOMER which uses a cumulative hypergeometric distribution to score motif enrichment in the target set compared to the background set. The p-value is not corrected for multiple testing.