Fig. 3

Pathway regulation by methylation and hydroxymethylation marks in normal prostate and prostate cancer. a Representative example of an enrichment map generated using Cytoscape depicting annotations significantly enriched for genes exhibiting intronic hydroxymethylation and highest tier expression levels in 22Rv1 alone as compared to all genes detected in both cell lines via hMeSeal-Seq. Annotated using the GREAT hypergeometric test over regions (p value < 0.05, FDR < 0.1, Jaccard’s similarity coefficient < 0.25). Left: select clusters of related pathways (nodes) in the enrichment map are highlighted (clusters identified using MCODE). Right: zoom in to signaling pathway enrichment map cluster. Below: pathway enrichment annotations from GREAT for hydroxymethylation within RWPE-1 cells, overlapping (b) exonic or (c) intronic regions and hydroxymethylation within 22Rv1 overlapping (d) intronic or (e) intergenic regions. Pathways further represented by genes within the highest (high expression) and lowest tier of expression (low expression)