Fig. 6

Network modeling of macrophage polarization. Application of NetAct to induced macrophage polarization via drug treatment in mice using RNA-seq data. a Experimental expression and activity of enriched TFs. b PCA projection of genome-wide gene expression profiles. Different point shapes indicate the time after treatment, and colors indicate treatment types c PCA projection of gene activity of enriched TFs. d Inferred TF regulatory network. Blue lines and arrowheads represent the gene activation; red lines and blunt heads represent the gene inhibition. e PCA projection of simulated gene activity of inferred network colored by mapping each model back to experimental data. f 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 mapped experimental conditions. The color legend of the heatmap is at the bottom