Figure 5

Importance of marginal and interaction effects from five marks, and their enrichment in different chromatin states, for explaining gene expression level differences between primates. (A) The left panel lists marginal (M) or interaction terms (I2 to I5) among the five marks, where each row represents an interaction term and each column represents the presence (black) or absence (grey) of a particular mark effect for that interaction term. For example, the first row represents the marginal effect of H3K4me1, and the sixth row represents the interaction effect between H3K4me1 and H3K4me3. The right panel lists the corresponding PIP of each term between any pairs of primates for DE genes classified with different FDR cutoffs. (B) The left panel lists marginal (M) or chromatin state-specific terms for 15 chromatin states (S1 to S15) near TSSs, where each column represents the presence (black) or absence (grey) of a particular mark effect for that term. For example, the sixth row represents the state-specific effect of H3K4me1 in chromatin state S1. The right panel lists the corresponding PIP. The PIP measures the importance of each interaction term with higher values indicating higher significance. Mark enrichment level differences and mark enrichment level differences inside chromatin states within ±2 kb regions near TSSs were used for fitting. C, chimpanzee; H, human; R, rhesus macaque. M, marginal effects; I2, interaction term between pairs of marks; I3, interaction term among three marks; I4, interaction term among four marks; I5, interaction term among five marks; S1, active promoter; S2, weak promoter; S3, poised promoter; S4, strong enhancer; S5, strong enhancer; S6, weak enhancer; S7, weak enhancer; S8, insulator; S9, transcription transition; S10, transcription elongation; S11, weak transcription; S12, repressed; S13, heterochroma/lo; S14, repetitive/copy number variation; S15, repetitive/copy number variation.