Fig. 3
From: Genome-wide profiling of transcribed enhancers during macrophage activation
Stimuli-responsive genes and enhancers. a Time-course data used in this study. b Enhancer and gene sets. E1 and E2: M(IFN-γ)- and M(IL-4/IL-13)-responsive enhancers regulating M(IFN-γ)- and M(IL-4/IL-13)-responsive genes (G1 and G2), respectively; E1′ and E2′: M(IFN-γ)- and M(IL-4/IL-13)-responsive enhancers regulating non-stimuli-responsive genes; G1′ and G2′: M(IFN-γ)- and M(IL-4/IL-13)-responsive genes not regulated by stimuli-responsive enhancers. Black arrows denote regulatory associations between stimuli-responsive enhancers and genes; of all previously defined significant associations, here we retained only those with positive correlation of expression in the corresponding subset of macrophages. c GO biological process terms enriched for G1 and G2 genes (all terms with FDR < 0.05 for G1; six terms with the lowest FDR for G2 are shown); dashed lines indicate FDR = 0.05. d Expression of stimuli-responsive enhancer eRNAs (upper panel) and genes (lower panel) unique to M(IFN-γ) or M(IL-4/IL-13). Statistical significance was determined by Wilcoxon signed-rank test, asterisks indicate p value < 10−5. e Correlation of time-course expression of M(IFN-γ)-responsive (upper panel) and M(IL-4/IL-13)-responsive (lower panel) enhancers and genes. Vertical dashed lines show median values