Fig. 3

Tissue specific and ubiquitous factors have distinct localization and regulation preferences. A Violin plots showing the GC content of the TF motif (PSSM) of ubiquitously shared TFs (pink), tissue specific TFs (purple), and all TFs (gray). B Bar plot showing that enhancers (orange) are far more tissue specific than promoters (blue) which tend to be on in all tissues. C Set of consensus bidirectional regions in embryonic stem cells containing a centered motif for the tissue specific Nanog (left) or the ubiqitous KLF12 (right), colored (promoter: blue, enhancer: orange) by presence or absence across multiple tissues (x-axis). Across 662 regions containing Nanog in ESC cells, 86.1% of regions are enhancers, with some being shared (bottom, solid orange) and others being more tissue specific (middle, mostly white). Across the 6388 KLF12 containing regions in ESCs, 70.3% are promoter regions. D Fraction of ChIP-seq binding sites at the 5\(^\prime\) end of genes (promoter, blue) or at distal regulatory regions (enhancers, orange) for ubiquitous TFs (pink) and tissue specific TFs (purple) [61, 62]. E Motif displacement score as a heatmap (darker is higher) for ubiquitous TFs (pink) and tissue specific TFs (purple)