Figure 4

Binding site retention is correlated with binding strength and vicinity to adipogenic genes. C/EBPα and PPARγ binding sites were assigned to the closest TSS of a cluster gene within 100 kb. Cluster 5 contains binding sites assigned to genes with no significant expression change, and cluster 6 contains binding sites >100 kb from the closest gene. (A) Bar diagrams representing the fraction of retained C/EBPα (blue) and PPARγ (red) bars, broken up by assigned expression cluster. The numbers above the bars represent the total number of retained binding sites in that cluster. *P = 2.2*10^-16 (clusters 3+4 vs. all other clusters (Fisher Exact Test)). (B) Complementary violin plots (see Fig. 3B for explanation) showing the distribution of tag enrichment in orthologous human regions, broken up by expression cluster, C/EBPα in red and PPARγ blue. *P = 2.9*10^-5 (cluster 4 vs. all clusters (Wilcoxon test)); #P = 4.55*10^-5 (cluster 3 vs. clusters 1+2+5+6 (Wilcoxon test). (C) Violin plots showing the distribution of tag counts in mouse binding regions, broken up by expression cluster, C/EBPα in red and PPARγ blue. *P = 1.643*10^-14 (clusters 3+4 vs. all other clusters (Wilcoxon test)); #P= 5.315*10^-6 (clusters 3+4 vs. clusters all other clusters (Wilcoxon test)) (D) Correlation between retention of mouse sites in human and binding strength in mouse measured by the number of ChIP-seq tags. Mouse binding sites were divided into four groups from low to high ChIP-seq density (x-axis), and we investigated what fraction of these sites were retained in human (y axis). Numbers above the bars correspond to the total number of retained mouse sites in human.