Fig. 5

Stimulus responsive TFs utilize distinct regions to achieve equitable stimulus response across tissues. A Scatter plot of the percentage of ChIP-seq sites within promoters (x-axis) vs. the GC content of the TF motif (PSSM, y-axis) for ubiquitous (pink), tissue specific (purple), and stimulus reponsive (green) TFs. B Comparing the transcription level (RPKM) of the gene encoding the TF NF\(\kappa\)B (x-axis) and MD-score (y-axis). Significant ON-UP instances of NF\(\kappa\)B are colored green and labeled with the stimulus. Inset is the PSSM for NF\(\kappa\)B2. C Bidirectional regions with a centered NF\(\kappa\)B2 motif from TNF\(\alpha\) treated cells (larger font in B, four tissues). Enhancer regions in orange and promoters in blue. Across 2302 regions with NF\(\kappa\)B2 motif instances, 77.5% are classified as enhancers. Of the enhancers, 1406 (78.9%) are unique to a given tissue type. Other subunits of NF\(\kappa\)B shown in Additional file 1: Fig. S14. D Heatmap of NF\(\kappa\)B target genes (y-axis) across the four tissues in (C) (heart, intestine, lung, prostate). Upregulated (green); gold (downregulated). E Upset plot of promoter regions (n = 519) shown in (C) where 42.0% are shared across all tissues (teal) and 81.0% are shared between at least two tissues. Numerous NF\(\kappa\)B target genes (teal text) are labeled. Three target genes (NF\(\kappa\)B2, REL, and RELB, bold) are three subunits of the NF\(\kappa\)B TF complex