Fig. 5

Network modeling of TGF-β-induced EMT. Application of NetAct to an EMT in human cell lines using time-series microarray data. a Experimental expression and activity of enriched transcription factors. b Inferred TF regulatory network. Blue lines and arrowheads represent the gene activation; red lines and blunt heads represent gene inhibition. c The relationship between SMAD3 gene activity and the first principal component of the activity of all network genes from RACIPE simulations. d Hierarchical clustering analysis of simulated gene activity (with Pearson correlation as the distance function and Ward.D2 linkage method). Colors at the top indicate the two clusters from the simulated gene activity. The blue cluster represents the mesenchymal state, and the yellow cluster represents the epithelial state. The color legend for the heatmap is at the bottom right. e Knockdown simulations of the TF regulatory network. The bar plot shows the proportion of RACIPE models in each state (epithelial or mesenchymal) for the conditions of the knockdown of every TF