Fig. 3
Loss of E2F4 leads to genome-wide changes in gene expression. a Volcano plot of changes in gene expression upon E2F4 loss in mouse ES cells; y-axis represents -log10 transformation of p-value and x-axis represents log2 transformation of fold change. Red circles represent significantly changed genes (q-value < 0.05) while orange circles represent significantly changed genes with a fold change > 0.5 (log2). b Overlap between E2F4 targets in mouse ES cells and genes differentially expressed in E2F4KO (KO)cells with respect to wild-type. c GO terms for biological processes enriched in genes downregulated in E2F4KO cells (q-value < 0.05, fold change > 0.5 (log2)). GO terms were filtered for redundancy through REVIGO and the top 20 most significant are shown. d RT-qPCR validation of differentially expressed genes. Expression of downregulated genes in WT (dark green) and E2F4KO cells (light green); and upregulated genes in WT (pink) and E2F4KO cells (light pink), was normalized to Gapdh expression and then to expression levels in WT cells (unpaired t-test was performed with all individual data points from n = 2–4 biological replicates with 2 WT and 2 E2F4KO clones). Data shown as the mean and standard error of the mean
