Knockouts affect downstream expression of genes on the recovered regulatory paths. (A) The six proteins from different regions of the signaling network were selected for deletion. The short network model, reproduced from Figure 2B, is shown here, and the positions of knocked-out genes are highlighted with red boxes. (B) Five knockouts significantly affected the genes assigned to the regulatory paths in the short model. Numbered paths are annotated with the knockouts where we found significant overlap between path members and knockout-affected genes. (C) The subnetwork affected by the ASF1 deletion. Only the relevant subset of the downstream TFs is shown, and the edges connecting Asf1 to the TFs are omitted for clarity. (D) The seven TFs predicted to control path 1's split from path 2 are displayed above path 1. All seven are downstream from Asf1 in the oriented network.