Fig. 1

Differential methylation analysis. a Mean methylation values of the good and poor prognosis groups in a smoothed colour density representation plot. Sites with FDR-corrected p values < 0.2 and absolute beta value difference > 0.1 are marked in red. b Distribution of the localization of differentially methylated CpG sites (DMS) hypermethylated (n = 100, top) or hypomethylated (n = 302, bottom) in the poor prognosis group relative to the good prognosis group, in relation to CpG islands. c Enrichment analysis of the hypermethylated (left) and hypomethylated (right) DMS using 7-state ChromHMM data for PC3 and LnCaP tumour cell lines and prostate epithelial cells (PrEC) [9]. The size of the circles demonstrates the significance of enrichment, while their colour represents the strength and the direction of the enrichment (red: enriched, blue: depleted). The black circle outline indicates significant results. d Pathway analysis of genes associated with the hypermethylated (top) and hypomethylated (bottom) DMS. GREAT tool was used to assign genes to CpG sites. The shade of blue shows the significance of the enrichment, while the bars represent the strength