Fig. 4

Twenty-five top-ranked differentially methylated CpG sites in fusion-positive versus fusion-negative PCa. a Volcano plot of DNA methylation. Differentially methylated CpGs (FDR Q-value <0.00001; n = 27,946) are displayed in green or red. The 25 red-labeled CpGs had a mean methylation difference of at least 25 % between tumor types, and the figure shows the genes these CpG sites map to. Four of the 25 CpGs were intergenic. b Unsupervised clustering using the 25 top differentially methylated CpG sites (rows) with FDR Q-value <0.00001 and a mean methylation difference of at least 25 % between prostate tumor types, in our cohort. The columns represent the prostate tumor samples (fusion-positive is shown under the red bar and fusion-negative is shown under the green bar). Higher methylation levels are displayed in red and lower methylation levels are shown in blue (white is intermediate). Two main clusters were identified, one that consisted primarily of fusion-positive tumors (89 %) and the other that consisted mostly of fusion-negative tumors (87 %). c Unsupervised clustering using the top CpG sites in TCGA (same approach as in b). One of the CpG sites (GREM1 cg17312492) was not represented in TCGA data, and the analysis therefore only included 24 CpG sites. Similar to our results, clustering using these CpG sites clearly separated fusion-positive from fusion-negative PCa. One of the two clusters contained 89 % of fusion-positive tumors and the other cluster contained 95 % of fusion-negative tumors