Fig. 4

Aberrant methylation in CL. a Frequently hyper- or hypomethylated genes in PCa⁷ that are also hypermethylated (purple) or hypomethylated (orange) in the CL-CB and CL-NL comparisons. b Overlap between the DMRs identified in the CL-CB and CL-NL comparisons. P-values derived from Fisher’s exact test. c Clustering of the gene ontologies (biological process) enriched in DMRs common between the CL-CB and CL-NL comparisons based on information similarity. Each circle shows an individual GO term enriched in regions hypermethylated (purple), hypomethylated (orange) or both (green), the size of the circles is proportional to the enrichment p-value. The two main clusters of GO terms determined by k-means are highlighted (light blue and pink), and named after the most frequent terms. d Heatmap showing scaled methylation values (β-values) of probes overlapping the DMRs common to the CL-CB and CL-NL comparisons in the PCa samples (magenta) and matched normal samples (green) within the TCGA dataset. Hierarchical clustering based on Euclidean distances of the unscaled values and complete linkage. The dark green and grey clusters were generated by cutting the tree at the first bifurcation. e Heatmap showing scaled methylation values (β-values) of probes overlapping the DMRs common to the CL-CB and CL-NL comparisons in the PCa samples (matched normal samples not included) of the TCGA dataset. Hierarchical clustering based on Euclidean distance of the unscaled values and complete linkage. The dark green and grey clusters are generated by cutting the tree at the first bifurcation