Application to pathogen infection experiments | First, it has been studied and validated in great detail [26—28] , such that the available signaling network from the KEGG database [22] can be used as a reliable source to compare to. |
Application to pathogen infection experiments | Nodes of KEGG pathways can contain several genes. |
Application to pathogen infection experiments | We selected genes such that they are all assigned to different KEGG nodes using a weighted maximum bipartite matching of low off-target siRNAs and unique KEGG nodes. |
Author Summary | Comparing the learned network to the known KEGG pathway of the genes shows that our method recovers networks significantly better than classical nested effects models without capturing of hidden signaling. |
Discussion | Before comparing a network to the corresponding KEGG pathway, we also built its transitive closure. |
Simulation study | We generated 30 network structures with 5 signaling genes, randomly sampled from KEGG pathway maps [22] as previously described in [6]. |