Extended Data Fig. 8: MSigDB gene set enrichment analysis.
From: BET bromodomain inhibitors regulate keratinocyte plasticity
(a) MSigDB gene set enrichment for genes significantly differentially expressed in keratinocytes with 6 h 125 nM NVS-BET-1 treatment versus DMSO control. Left panel shows enrichment of downregulated genes and right panel enrichment of upregulated genes using a hypergeometric test (b) Genes (highlighted in dark blue) from the ‘C2_ONDER_CDH1_Targets_2_DN’ gene signature (top gene set in Extended Data Fig. 4a left panel) projected onto global gene expression changes (RNA-seq, left panel) or onto gene-associated (based on proximity) BRD4 ChIP-seq peaks (right panel) after 6 h exposure to 125 nM NVS-BET-1 versus DMSO control (c) Genes (highlighted in dark blue) from the ‘C2-HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP’ gene signature (top gene set in Extended Data Fig. 4a right panel) projected onto global gene expression changes (RNA-seq, left panel) or onto gene-associated (based on proximity) BRD4 ChIP-seq peaks (right panel) after 6 h exposure to 125 nM NVS-BET-1 versus DMSO control. ChIP-seq differential analysis was performed using DiffBind with DESeq2 (abs(log2FC) > 1 & p-value < 0.01). RNA-seq differential analysis was performed on the counts per million (CPMs) using a limma voom workflow with abs(log2FC) > 1 & adjusted p-value < 0.01. Dotted red lines indicate significance cut-offs.
