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Figure 4 | Genome Biology

Figure 4

From: Epigenetic modifications are associated with inter-species gene expression variation in primates

Figure 4

Differences in mark enrichment level correlate with differences in gene expression level between pairs of primates. (A) Differences in mark enrichment level is plotted against differences in gene expression level for sliding windows of genes (n = 200) ordered based on the differential expression effect size, for all genes. Differences in enrichment level were obtained in ±2 kb regions near TSSs and scaled to be between -1 and 1. All values are averaged across individuals and across genes in the window. (B) Proportion of variance in gene expression level differences explained (R squared) by mark enrichment level differences, for all pairwise comparisons among the three primates. Different linear models are fitted to account for individual marginal effects (five colored bars), combined marginal effects (grey bars), all first-order interaction effects in addition to marginal effects (black bars), and all chromatin state-specific effects in addition to marginal effects (white bars) of the five marks. The DE genes are determined based on an FDR cutoff of 5%. Enrichment level differences are obtained in ±2 kb regions. Error bars indicate standard deviation calculated across 20 split replicates. C, chimpanzee; H, human; R, rhesus macaque.

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