Information channels in protein interaction networks

Motivation: Recent advances in experimental techniques have generated larg amounts of protein interaction data, producing networks containing large numbers of cellular proteins. Mathe matically sound and robust foundations are needed for extensive, context-specific exploration of networks, inte grating knowledge from different specializations and faci litating biological discovery. Results: Extending our earlier work, we present a theoretical constr uct, based on random walks, for modelling information channels between selected points in interaction networks. The software implementation, called ITM Probe, can be used as a network exploration and hypothesis forming tool. T hrough examples involving the yeast pheromone response pathway, we illustrate the versatility and stabilit y of ITM Probe. Availability: www.ncbi.nlm.nih.gov/CBBresearch/qmbp/itm probe Contact: yyu@ncbi.nlm.nih.gov to whom correspondence should be addressed