Evaluation of differentially modified regions.
a) qPCR validation of differential H3K27me3 regions in rat heart tissue. The boxplots show the level of histone modifications for the five true positive regions that were not overlapping genomic deletions. Modification levels are measured as δCT values for the two rat strains BN and SHR. All differences are significant (t-test P<0.05). b-f) Barplots of −l
10(P) of Fisher’s exact test for overlap of differentially modified genes with differentially expressed genes for each of the methods. b) shows results for H3K27me3 in the rat strain comparison. c) shows results for H3K9me3 in the comparison of female and male mice. d-f) show results of the comparison of ENCODE cell lines H1-hESC and K562. Differential H3K9me3, H3K36me3 and H3K79me2 regions are compared to differential gene expression. g) shows results of the comparison of ENCODE cell lines H1-hESC and K562. Differential H3K27me3 regions are compared to genes with differential EZH2 levels.