Flood analysis reveals key pathways in directed weighted regulatory networks. (A) Disconnected nodes can be discarded based on their connectivity to inputs and outputs. (B) Direction of links can be used to discard nodes which do not regulate outputs directly or indirectly. (C) Flood analysis takes into account weights and signs of directed links and captures up- and down- regulation of nodes. Positive floods from inputs to outputs indicate the pathways that are active for a given scenario (a given set of inputs and outputs), the flood value in each link/node is a metric of that link/node importance.