Fig. 4

BET Bromodomain Inhibition Modulates Distinct Networks of Immune-Related Genes. a Top 20 upregulated and downregulated transcripts significantly altered by IFNγ significantly further modulated in the presence of 1uM JQ1 in DU145 cells. Scale represents log transformed FPKMs + 0.1, data are row normalized. b Gene set enrichment analysis (GSEA) using the Reactome database in EnrichR for top 20 genes whose expression is significantly altered by IFNγ and whose expression is upregulated by incubation with 1uM JQ1 in DU145 cells. Colors represent ranking based on combined enrichment score (a value calculated through multiplying log p-value and z-score), with highest enrichment scores in brighter shades. c GSEA using the Reactome database in EnrichR for top 20 genes whose expression is significantly altered by IFNγ and whose expression is downregulated by addition of 1uM JQ1 in DU145 cells. Colors represent ranking based on combined enrichment score, with highest enrichment scores in brighter shades. d Genes in DU145 cells significantly downregulated or upregulated with IFN-γ treatment whose expression is further modulated with JQ1 treatment. e Expression of immune-related genes, including Class I, Class II, and checkpoints, in DU145 cells across treatment conditions. Scale represents log transformed FPKMs + 0.1, data are row normalized. f Correlation matrix of immune-related genes in DU145 cells across treatment conditions. g Networks of immune-related genes, including Class I, Class II, and checkpoints, altered by JQ1 treatment. Lines indicate strength of connections between two genes, and size of node represents relative importance of gene in the network.p < 0.05 for all significantly differentially expressed transcripts. N = 3/group, repeated × 1