Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases
Fig 2
Small example network with unresolvable ambiguity.
The true network (A), KPs (diamonds), TFs (circles) and target gene ‘V1’. The resulting mRNA outputs from simulated KO experiments are shown in (B-F) and represents the data used for inference. A graph representing the cumulative (total) influence through all pathways is shown in (G), and the inferred regulatory interactions are shown in (H). The node value color scale applies to (B-F) where colors show mRNA log fold-change values for each knockout. The Edge value color scale shows the “true” regulatory weights in (B-F) and the inferred values in (H). The knockout protein is indicated with a red border and strike-through. Dotted edges indicate the direct effects that were removed by the knockout.