PReach: Reachability in Probabilistic Signaling Networks

Extracellular molecules trigger a response inside the cell by initiating a signal at special membrane receptors (i.e., sources) which is then transmitted to reporters (i.e., targets) through various chains of interactions among proteins. Understanding whether such a signal can reach from membrane receptors to reporters is essential in studying the cell response to extracellular events. This problem is drastically complicated due to the unreliability of the interaction data. In this paper, we develop a novel method, called PReach (Probabilistic Reachability), that precisely computes the probability that a signal can reach from a given collection of receptors to a given collection of reporters when the underlying signaling network is uncertain. This is a very difficult computational problem with no known polynomial-time solution. PReach represents each uncertain interaction as a bivariate polynomial. It transforms the reachability problem to a polynomial multiplication problem. We introd...

• Type: Journal
• Year: 2013
• Where: BCB
• Authors: Haitham Gabr, Andrei Todor, Helia Zandi, Alin Dobra, Tamer Kahveci
• Keywords: BCB 2013, Bioinformatics