Fig. 5

Trans effects are associated with a subset of differentially expressed TFs. a Volcano plot showing the differential expression of orthologous human and mouse TFs in hESCs and mESCs. Blue dots indicate significantly differentially expressed TFs (FDR < 0.01 and absolute log2 fold change ≥ 1). The top 2 most differentially expressed TFs in either direction are highlighted. b Plot showing the activating motifs significantly associated with trans effects (FDR < 0.05) that are also differentially expressed between hESCs and mESCs in the expected direction. Left: effect size associated with motif enrichment. Motifs that are associated with sequences more highly expressed in mESCs are > 0, and those associated with sequences more highly expressed in hESCs are < 0. Middle: log2 fold change in expression via RNA-seq. Right: enrichment of a given TF motif across biotypes, as determined by a hypergeometric test. Black dots denote significant enrichment (FDR < 0.05). c Relationship between trans effect sizes and the BACH2 and POU2F3 motifs. Trans effect sizes for sequences with motif and without motif. Trans effect sizes > 0 indicate higher activity in mESCs while effect sizes < 0 indicate higher activity in mESCs. p values shown are from two-sided Mann-Whitney tests. d Genome browser screenshot of an example locus showing a trans effect. Gray motifs correspond to TFs that are not differentially expressed between hESCs and mESCS; the purple motif, POU2F3, is differentially expressed. e MPRA activities in hESCs (orange) and mESCs (green) for the mouse locus shown in d. p value shown is the q value calculated by MPRAnalyze