Gene expression differences between humans and chimpanzees and their relationship with epigenetic differences. (A, left) The percentage of genes that show significant gene expression differences between humans and chimpanzees (red bars) and expected by chance (gray bars); (right) pie charts showing the percentages of human-specific (orange), chimpanzee-specific (purple), and unassigned (gray) gene expression differences sorted using combined gorilla and gibbon outgroup information. (B) The percentages of gene expression variance between humans and chimpanzees explained by promoter CREs (P) and enhancer CREs (E) coverage differences in each brain region shared between transcriptome (gene) and epigenome (CRE) data sets. (C) Normalized H3K27ac read counts for CREs located next to genes differentially expressed between humans and chimpanzees: (Left) The color of the dots shows the direction of the expression difference: (red) higher in humans; (blue) lower in humans. (Right) The box plots show distributions of CRE coverage in humans (orange) and chimpanzees (purple) for the corresponding dots. The significance of the coverage differences between humans and chimpanzees in a one-sided Wilcoxon test was shown by each dot's color gradient (left) and the asterisks (right): (***) P < 0.0005; (**) P < 0.005. The numbers indicate brain regions in accordance with the index shown in B. (D) Normalized H3K27ac read counts for CREs located next to genes showing human-specific gene expression changes. (Left) The color of the dots shows the direction of the expression difference, as in C. Each dot's shape represents nonhuman species: (circle) chimpanzees; (diamond) macaques. (Right) The box plots show the distributions of CRE coverage in humans (orange), chimpanzees (purple), and macaques (green) for the corresponding dots. The significance of the coverage differences between humans and nonhuman primates in a one-sided Wilcoxon test was shown by each dot's color gradient (left) and the asterisks (right): (***) P < 0.0005; (**) P < 0.005; (*) P < 0.05; (#) P > 0.05 as the gray dot shows. The numbers indicate brain regions in accordance with the index shown in B.
