Figure 3
Relating Module Membership to Epigenetic Regulation. The top 1000 genes with highest module membership in the black module (top row) and blue module (bottom row) are related to 3 epigenetic variables (corresponding to the 3 columns). The y-axis reports the proportion of top 1000 genes that are known to belong to the group of genes defined on the x-axis. Histone H3K4me3 trimethylation status is abbreviated K4, H3K27me3 trimethylation statys is abbreviated by K27. Promoters that are both H3K4 and H3K27 trimethilated in ES cells (denoted K 4&K 27) are thought to poise key developmental genes for activation upon differentiation [50, 51]. Note that genes with promoter CpG methylation are significantly (p = 2.0 × 10-14) under-enriched with respect to the top 1000 black module genes.