Extended Data Fig. 8: DMRs and CIMP in CPGEA.
From: A genomic and epigenomic atlas of prostate cancer in Asian populations
a, Recurrence of hypoDMRs. There were 1,172 hypoDMRs were shared by at least 10 tumours (red line). b, Recurrence of hyperDMRs. There were 4,214 hyperDMRs were shared by at least 10 tumours (red line). c, Genomic location of the union set of hypoDMRs and recurrent hypoDMRs. The innermost circle represents the reference genome background. d, Genomic location of the union set of hyperDMRs and recurrent hyperDMRs. The innermost circle represents the reference genome background. e, MSigDB perturbation enrichment analysis of recurrent hypoDMRs (n = 1,172) using GREAT87. f, Gene Ontology (GO) enrichment analysis of recurrent hyperDMRs (n = 4,214) using GREAT. The top 20 GO biological process terms are shown. g, Scatter plots of example epigenetically silenced genes. Each dot represents a normal sample (red), a tumour without a silenced gene (blue), or a tumour with a silenced gene (black). TPM, transcripts per million. h, Heat map of CIMP-CGI methylation levels. Rows represent CIMP-CGIs, and columns represent samples. Tumours (right) were clustered by CIMP-CGI methylation levels, and matched normal samples (left) were sorted in the same order. CIMP-CGIs were sorted by chromosome and genomic coordinates. The top panel shows clinicopathological features of patients (as in Fig. 1), genetic alterations, including fusions and coding mutations, and other molecular phenotypes. i, Proportion of recurrent hyperDMRs overlapping CGIs. j, Association of CIMP+ tumours (n = 33) with gene mutation status. Red vertical line represents P = 0.05 (two-sided Fisher’s exact test). k, Kaplan–Meier plot of biochemical recurrence-free survival in patients with CIMP+ and CIMP− tumours. P values were determined by two-sided log-rank test. l, m, Correlation between epimutation burden and mutation (l) or CNA (m) burden. Spearman’s correlation coefficient ρ = 0.37, P = 2.5 × 10−7 for mutation burden, and ρ = 0.65, P = 1.2 × 10−23 for CNA burden. Each dot represents a tumour (n = 187).
