Supplementary Figure 4 : Evolutionary conservation of cCREs

Supplementary Figure 4 | Evolutionary conservation of cCREs

a, Density plots showing the distribution of PhastCons scores from the 100-way vertebrate alignment, stratified by cCRE class. Vertical bars indicate median values, which are also listed at right. P-value corresponds to pairwise, two-sided Wilcoxon test with FDR correction. b, Line plots of average phyloP conservation scores (100-way vertebrate alignment) +/- 250 bp around the center of each cCRE, stratified by cCRE class. c, As in b, but using phyloP scores from the 240-way mammalian alignment. d, Heatscatter plot showing the distribution of human ENCODE4 cCREs based on their alignment across Zoonomia mammalian genomes. N1 denotes the number of species in which ≥90% of a cCRE aligns; N2 denotes the number of species in which ≤10% of a cCRE aligns. Rectangles indicate predefined groups: Group 1 (G1), highly conserved (N1 ≥ 120, N2 ≤ 25); Group 2 (G2), actively evolving (20 ≤ N1 ≤ 50, N2 ≤ 120); and Group 3 (G3), primate-specific (N1 ≤ 50, N2 ≥ 180). The percentage of cCREs in each group is indicated. e, Heatscatter plot as in d, but for size-matched non-cCRE regions. f, Heatscatter plots as in d, stratified by cCRE class.