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Table 1 Locus-specific hydroxymethylation changes in cancer. 5hmC changes were described by the overlap of 5mC and/or 5hmC marks between cell lines. Overlapping 5mC or 5hmC marks were compared to the overall distribution of each mark within each cell line to determine significant differences

From: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis

Differential 5mC/5hmC status in PCa Prostate cell type (normal vs. cancer) Overlapping methylation marks Genomic region
Intergenic Genic Exonic Intronic Promoter CpG Island RWPE-1 DNaseI hypersensitive sites
5hmC “Absent” RWPE-1 5hmC 0.051 0.666 <0.0001*,** 0.005*,*** <0.0001*,** <0.0001*,** <0.0001*,**
22Rv1 5mC <0.0001* 0.311 0.002*,** 0.001*,*** <0.0001*,** <0.0001*,** <0.0001*,**
5hmC “Retained” RWPE-1 5hmC 0.302 0.01 0.039 0.169 0.487 0.593 0.067
22Rv1 5hmC 0.013 0.547 0.452 0.834 0.115 0.001* 0.944
5hmC “Gained” RWPE-1 5mC 0.003*,*** 0.975 0.175 0.834 0.5 <0.0001*,** 0.007*
22Rv1 5hmC <0.0001*,*** 0.026 0.025 0.538 0.71 <0.0001*,** 0.511
  1. *Significant p values as determined by the chi-square test with Bonferroni correction for multiple testing applied; **5hmC is significantly more likely to be absent, gained, or retained within the given region than expected; ***5hmC is significantly less likely to be absent, gained, or retained within the given region than expected