Figure 6: Epigenomically distinguishing genes are enriched for differential expression.

By analysing expression of genes that our method identifies as being part of distinguishing gene and chromatin state combinations, we find that our method both recaptures differential gene expression and identifies distinguishing epigenetic context not captured by differential gene expression. (We performed this analysis on the 12 comparisons that produced distinguishing epigenomic features.) (a) Overall, identified genes are more differentially expressed than non-distinguishing genes, although <50% of the genes identified are significantly differently expressed. (The three comparisons that resulted in no differentially expressed genes are excluded.) (b) In every comparison of our nine remaining comparisons, our identified genes were significantly enriched for differentially expressed genes overall (as designated by asterisks), based on calculation of the log odds ratio and the corresponding 95% confidence intervals, as shown by the error bars. (P<0.003 in all cases, two-sided z-test) (c). After correcting for covariates in expression data, ChromDiff identifies all of the differentially expressed genes in two of the remaining four cases. (The eight comparisons that yielded no significant expression differences are excluded.)