Figure 3 : Association between rearrangement breakpoints and genome-wide transcriptional/histone marks in prostate cancer.

From: The genomic complexity of primary human prostate cancer

Figure 3

ChIP-seq binding peaks were defined previously for the TMPRSS2ERG positive (ERG-positive) prostate cancer cell line VCaP35. For each genome, enrichment of breakpoints within 50 kb of each set of binding peaks was determined relative to a coverage-matched simulated background (see Methods). TMPRSS2–ERG-positive prostate tumours are in black; ETS fusion-negative prostate tumours are in white. Enrichment is displayed as the ratio of the observed breakpoint rate to the background rate near each indicated set of ChIP-seq peaks. Rearrangements in ETS fusion-negative tumours are depleted near marks of active transcription (AR, ERG, H3K4me3, H3K36me3, Pol II and H3ace) and enriched near marks of closed chromatin (H3K27me3). P-values were calculated according to the binomial distribution and are displayed in Supplementary Fig. 5 and Supplementary Table 6. *Significant associations passing a false discovery rate cut-off of 5%.