Fig. 2

Forty percent of orthologous regulatory elements show significant cis effects. a Schematic depicting the definition of a cis effect: MPRA activity differences between human sequences and mouse sequences while keeping the cellular environment constant. b Volcano plot showing the cis effect sizes (log2 fold changes in activity between sequences in hESCs (left) and mESCs (right)) of orthologous sequences (black) and null differential controls (gray). Horizontal line depicts an empirical FDR cutoff of 0.1, calculated using null differential controls (see the “Methods” section). c Count of orthologous sequence pairs with significant cis effects in either hESCs or mESCs. d Scatter plot showing the cis effects measured in hESCs (x axis) and mESCs (y axis) for a given sequence pair, colored by whether they are significant in hESCs (orange), mESCs (green), both (black), or neither (gray). Spearman’s rho and number of sequences are shown. e Absolute cis effect sizes across biotypes, broken up into non-conserved TSSs (blue) and conserved TSSs (gray). p values shown are from a two-sided Mann-Whitney test. f Same as d, but this time comparing differences across biotypes. p values shown are from a two-sided Mann-Whitney test