Fig. 4

Integration of ATAC-seq and RNA-seq. (A) Gene expression changes in differential accessibility regions. (B) Overlap of genes with differential expression and genes with differential accessibility. (C) Correlation of changes between ATAC-seq and RNA-seq. (D) Functional analysis of genes associated with both up-regulated expression and more accessible regions in PDGF-BB treatment samples and associated with both down-regulated expression and less accessible regions in PDGF-BB treated samples. The numbers outside of the table are the size of each set of hallmark genes (on the left of the table) and up/down regulated genes (DEGs, on the top of the table). The numbers inside the table are the number of genes overlapping between the hallmark gene sets and DEGs. Significantly (p < 0.01) overrepresented hallmark gene sets in genes associated with more open regions are colored red, while significantly overrepresented hallmark gene sets in genes associated with more closed regions are colored blue