Fig. 4.

Workflow of the regulatory network inference. For each TF, a two-step profile of its targets is created. This profile includes the TF’s targets and its targets’ targets. If a TF is differentially expressed the regulatory subnetwork inferred consists of two types of interactions. First, the TF/target gene pairs when both TF and target gene are differentially expressed (e.g. Regulator-B interaction) and the TF/target-gene/target-of-target-gene when TF and target of target are differentially expressed, regardless of the expression status of the first-level target (e.g. Regulator-B-B2, Regulator-C-C1). See Methods for more details