Fig. 3

Transcription factor binding site evolution. a The number of liver-specific TFs (56 in total) with at least one bTFBS in the promoters of the 30 ohnologs with one liver-specific up-shifted copy (Up) or one conserved copy (Cons). b Tissue expression of the 30 ohnolog pairs where one copy has evolved a liver-specific gain in expression (color bar: up-shifted copies are red and conserved copies are gray) and 22 liver-specific TFs predicted to bind at least one-third of the targets (purple). TFs are named according to their motif(s) in JASPAR. Liver-specific genes are defined as having liver expression levels in the 90% quantile and tau-scores > 0.6. Each gene (row) is scaled so that red signifies the highest expression across the tissues and blue the lowest. c Regulatory network reconstructed for the ohnologs and selected TFs from b using footprinting data. Ohnologs are represented by circles sized by their regulatory complexity (in-degree) and colored according to their evolutionary expression shift with red signifying up-shift and blue down-shift. TFs are represented by diamonds with the nine most up-shift-biased TFs shown. A directed gray edge means that the TF has at least one bTFBS in the promoter of the gene. A dotted undirected green edge connects ohnologs