Fig. 3

RNA sequencing analysis of Foxf2-dependent gene expression. a Venn diagram illustrating the overlap of significantly differentially expressed genes (p adjusted < 0.05, abs(log2 fold change) ≥ 1) between the epithelial and mesenchymal state (0 days vs 4 days siRNA control (siCtrl)) or for the Foxf2 perturbation (4 days siFoxf2 vs 4 days siCtrl). Highlighted in bold are genes whose change during EMT is reversed by Foxf2 knockdown. b Heatmap of gene expression from RNA-sequencing of epithelial control samples (untreated siCtrl NMuMG cells) and of siCtrl- or siFoxf2-treated NMuMG cells in the presence of TGFβ for 4 days. The sample order in the heatmap was obtained from an unsupervised hierarchical clustering, while rows (genes) were arranged according to the gene signatures derived from WGCNA. c The eigengene expression of the different gene signatures derived from WGCNA (see a) illustrates a general expression trend of all genes belonging to a gene signature. d IPA analysis of the brown and yellow gene signature. Shown in the bar plot are the significance ranges of pathways belonging to the most significantly enriched categories. The dotted red line indicates a p value of 0.05. Differential gene expression and gene signature memberships are reported in Additional file 1 (Table S1 and S2, respectively)