Extended Data Fig. 9: Molecular subtypes of prostate cancer.

a, Molecular taxonomy across eight cohorts based on seven important oncogenic drivers identified by TCGA. b, Mutation burden, CNA burden and epimutation burden across the four molecular subtypes in CPGEA. c, Key CNA events, CIMP and fusion events across the four subtypes. ERG fusion-positive genes were combined results from Meerkat, SOAPfuse and high expression samples. d, Annotation of each molecular subtype. e, Kaplan–Meier plot of biochemical relapse-free survival for iCluster subtype D compared to the other three iCluster subtypes. P values were determined by two-sided log-rank test. f–h, Clustering of tumours using single datasets, using RNA-seq analysis (f), DNA methylation (g), and miRNA data (h). h, Rows represent miRNAs and columns represent tumours. The top panel shows clinical features of patients (as in Fig. 1) along with four miRNA clusters and four iCluster subtypes. i, Violin plots of mutation, CNA and epimutation burdens for four miRNA clusters. Mutation burden, P = 0.85, 0.43, 0.61, 0.58, 0.24 and 0.16, for the comparison between miRNA clusters of 1–2, 1–3, 1–4, 2–3, 2–4 and 3–4, respectively. CNA burden, P = 5.9 × 10⁻⁶, 0.00025, 0.29, 0.045, 1.3 × 10⁻²⁶, and 4.1 × 10⁻⁵, in the same order. Epimutation burden, P = 0.0052, 0.090, 0.24, 0.20, 6.1 × 10⁻⁵ and 0.0080, in the same order. P values determined by two-sided Mann–Whitney U-test. Each dot corresponds to a tumour sample belong to miRNA cluster 1 (n = 21), 2 (n = 37), 3 (n = 34), or 4 (n = 13). j, Box plots of miRNA expression levels in normal samples and four miRNA-based tumour clusters (cluster 1 (n = 21), 2 (n = 37), 3 (n = 34), or 4 (n = 13)). Box plots are as in Fig. 4b. k, Kaplan–Meier plot of biochemical recurrence-free survival in patients with tumours belonging to miRNA cluster 2 or other clusters. P values were determined by two-sided log-rank test. Primary tumours without any treatment were included.