Fig. 3

PAF1 modulates the expression of genes related to immune mechanisms and host machinery. A The log2 foldchanges of immune genes (GO: 0002376) upregulated (log2 foldchange > 2) following each stimulus in ncgRNA cells (relative to the mock) are plotted. These genes are mapped to their counterpart log2 foldchanges in PAF1 KO cells. A paired Wilcoxon signed rank test with Bonferroni correction was performed to assess significant changes between the distributions of foldchanges. B GSEA was performed on gene expression data from PAF1 KO (relative to ncgRNA) for each stimulus, wherein genes were ranked by a weighted statistic for log2 foldchange and adjusted p-value. Significantly enriched Reactome pathways (p.adj < 0.05) were analyzed for overlap amongst stimuli and the results shown on an upset plot. The number of pathways that overlap across all stimuli is highlighted in yellow. Filled dots indicate which stimuli shared enrichment for the given number of pathways. C, D GSEA random walks with the running total enrichment score (ES) were plotted for Reactome pathways found to be negatively (C) or positively (D) enriched across stimuli. Colors differentiate stimuli on each plot. Numbers listed in the upper-right corner of plots indicate the size of the gene set shown. The full GSEA output is available in Table S2B