Direct regulation between genes is defined based on causal attribution analysis and indirect regulation of an induced gene is defined if a gene is differentially expressed regardless of whether attribution analysis indicated a direct regulatory relationship. A. Edges between both genes with induction experiments and predicted regulators were formed based on regulatory interactions predicted from individual experiments (as shown in Figure 3C). For this visualization, major regulators selected as per Figure 3C are rooted to the induced TF regardless of whether they were directly or indirectly regulated by this gene. Predicted regulators are linked to GO categories based on having a significant overlap with their predicted targets. Similarly, genes with an induction experiment are linked to GO categories based on overlap of either direct or indirect targets with GO categories. Validated nodes (green) are genes where validation experiments confirmed a significant overlap between measured gene-regulator connections and model-predicted coefficients. Invalidated nodes (red) are genes where validation experiments failed to confirm model-predicted coefficients. B. Local networks based on upstream direct/indirect regulators and downstream direct targets of three validated regulators. 