Fig. 6

Predicted enhancers associated with PAF1-dependency and the innate immune response. A Enhancers associated with the core PAF1-dependent upregulated (orange) and downregulated (magenta) genes are displayed on the human genome. Enhancer chromosomal regions were extracted and plotted in 0.5 Mb bins. The extent these regions overlapped was calculated with a Jaccard statistic. B Volcano plots show results of relative enrichment analysis on extracted enhancers. Significantly enriched motifs (E < 0.05, enrichment ratio > 2) are colored. The top 10 enrichment ratios for known motifs are highlighted for each set. C Venn diagram shows overlap of enriched motifs associated with upregulated and downregulated genes. D Manhattan plot displays significant (p.adj < 0.05) motifs associated with GO-BP immune response terms (GO: 0006955). Motifs were submitted to GOMo and enriched for correlated terms, correcting for false-discovery rate with Benjamini-Hochberg method. Color indicates whether the enriched motif was associated with downregulated (magenta) or upregulated genes (orange) alone, or if it was shared between them (grey). The analytical pipeline for these analyses is further clarified in Fig. S3A