Fig. 2

Correlation between locus-specific methylation or hydroxymethylation and gene expression. a Validation of hMeSeal-Seq results by hMeDIP-Seq. Left: 62.6 % of genes detected as hydroxymethylated in RWPE-1 by hMeSeal were also detected as hydroxymethylated using hMeDIP, while 2.3 % of peaks from these genes were called in exactly the same chromosomal location using both methods. Right: genomic feature distribution for peaks called in the same regions in both hMeDIP- and hMeSeal-seq. Some features may overlap each other, and thus one peak may be accounted for more than once. b Total peaks called from sequencing data in normal and prostate cancer cell lines. Peaks called across three replicates for MBD-Seq or within one single replicate for hMeSeal-seq. c–f Differentially methylated (c, d) and differentially hydroxymethylated (e, f) regions for both cell lines stratified by genomic feature. Bar graphs depict the relative abundance of each mark within each of three expression tiers from microarray analysis. Asterisks represent significant p values (p < 0.05, chi-square test for trend) indicating correlation between the presence of 5mC or 5hmC marks in a given region and gene expression within each cell line. Upward trend of bars, when significant, indicates a positive correlation of a locus-specific mark with gene expression. Significant downward trend indicates negative correlation