RNA expression and integrated analyses. (A) Heat map for unsupervised hierarchical clustering of all 13 506 genes expressed at least once in 1 of the 8 samples. Untreated and TPA-treated HEL cells clustered together, as expected. Changes in gene expression between the untreated and MRTFA^OE cells are also apparent. (B-D) Volcano plots showing significantly upregulated (red) and downregulated (blue) genes for each of the comparison groups. Several significant genes are labeled on each plot. Bold numbers at the top of each plot represent the number of genes upregulated and downregulated. The dotted vertical lines represent thresholds of twofold change (log₂ = 1) in panel B and 20% in panel D. The false discovery rate (FDR) thresholds were set at ≤0.05, represented by the dotted horizontal lines. Green dots represent genes that reached statistical significance but changed by less than twofold (B-C) and <20% (D). (E-G) Volcano plots representing the expression of genes that have an associated SRF peak with labeling as in panels B-D.