Construction of signaling pathways from PPI and RNAi data using Linear Programming

For the reconstruction of signaling pathways from RNAi data, an integer linear optimization model is proposed. The aim is to reconstruct the signaling network from the given protein protein interaction (PPI) network satisfying RNAi data by making minimum changes on the given network. For evaluation, 1000 reference PPI networks each with seven, eight, or nine proteins, and RNAi data for each of the regular proteins in the network were generated randomly. The solution was examined to have a general overview about reconstruction of signaling networks from RNAi data by using the proposed method.