Fig. 6

TGF treatment induces a core of TNF regulated genes. a Venn diagram of the overlap of TGF regulated genes (CMvsCE) with those induced by TNF at 1 h (T1EvsCE) and 12 h (T12EvsCE) in hSAECs. The overlapping genes between TGF state (CMvsCE) and both or either of TNF 1 h or 12 h were considered for further analysis. This gene set amounts to 547 genes. b. Heat map of TNF regulated EMT genes. a clustered image heatmap of a normalized matrix was created that correlates gene expression pattern of 249 genes to the time course in HSAECs upon stimulation by TNFα and TGFβ. For each gene, mean and standard deviation were calculated from their expression values across the time course and were normalized to unstimulated HSAECs. Z-score transformation was applied for each gene [5]. Hierarchical clustering was performed using an average-linkage clustering algorithm across the time points in the absence or presence of stimulants. The cluster tree of genes is represented on the y-axis, and time-points and stimulants are shown on the x-axis. Each block of red or green represents a high positive or negative correlation between the gene expression and the stimulant under a specific time point. The list of genes in each cluster are shown in Table 8. (C) Top 10 pathways uniquely associated with TNF-induced genes in epithelial cells (top) and mesenchymal cells (bottom). Primary y-axis is the Ratio of Enrichment (R); secondary axis is adjusted P value (described in Fig. 5)