Skip to main content
Fig. 1 | Genome Biology

Fig. 1

From: Cis and trans effects differentially contribute to the evolution of promoters and enhancers

Fig. 1

MPRA in human and mouse ESCs parallels endogenous gene expression patterns. a Schematic depicting the definitions of a sequence ortholog and conserved/non-conserved TSSs. Sequence orthologs are TSS regions whose sequences can be reciprocally mapped to the other species. Conserved TSSs are a subset of sequence orthologs that also overlap a TSS in the other species (defined as having ≥ 10 CAGE reads in ≥ 1 sample), whereas non-conserved TSSs do not. b Percentage of human-to-mouse sequence orthologs and conserved TSSs broken up by biotype. c Schematic of MPRA design. Tile 1 overlaps the assigned TSS (114 bp upstream to 30 bp downstream) whereas tile 2 does not (228 bp upstream to 84 bp upstream). d MPRA activities of human (top) and mouse (bottom) TSSs in their native contexts, human ESCs and mouse ESCs, respectively, broken up by whether they have endogenous CAGE activity and then by biotype and compared to negative controls (random sequences) and positive controls (CMV promoter regions). e MPRA activities of TSS-overlapping tile (tile 1) compared to upstream tile (tile 2) across all human biotypes (top) and mouse biotypes (bottom). p values shown are from a one-sided Mann-Whitney test

Back to article page