Evolutionary divergence of induced versus constitutive antiviral gene expression levels between primates and rodents
Fig 7
Human-mouse divergence in dsRNA response is recapitulated at the chromatin level, in IFN response and across different cell types.
(A) Fraction of genes whose pattern of promoter activity agrees with gene expression, matching one of the 4 divergent groups (colored as in the legend) versus the fraction of genes among the rest of DE genes that display this pattern (in grey). For example, ~ 6% of human constitutive-low genes show the expected pattern at the chromatin level, and ~2% of all other DE genes show the same pattern (two left-most bars). FDR-corrected Fisher’s exact test P-values are shown. These tests show that the pattern of transcriptional response is recapitulated at the chromatin level in all four groups since the fraction of genes whose chromatin accessibility pattern agrees with the transcriptional pattern is higher than that observed in the set of all other DE genes (this is significant in three of four groups tested). (B) logFC distribution values based on DE analyses between human and mouse in dsRNA stimulation (before the arrow) and in IFN stimulation (after the arrow). In both cases the genes are partitioned into three boxplots based on three groups defined previously: “human constitutive-low”, “mouse constitutive-low” and “all other DE genes”. Thus, the same three groups of genes are shown before and after the arrow, but their FC values varies based on either dsRNA- or IFN-stimulation DE values. The analysis shows that the separation in logFC values in the dsRNA-stimulation between the three groups is also observed in the IFN-stimulation, suggesting similar transcriptional divergence between dsRNA response and IFN response. (C) The same as in B, but with basal conditions used in the DE analyses and showing: “mouse constitutive-high”, ‘human constitutive-high”, “all other DE genes”. In both B and C, FDR-corrected P-values are shown for one-sided Mann–Whitney tests, performed under the hypothesis that the FC distribution of the left group is higher than the right group.