Discovering pathways by orienting edges in protein interaction networks.

ABSTRACT: Modern experimental technology enables the identification of the sensory proteins that interact with the cells' environment or various pathogens. Expression and knockdown studies can determine the downstream effects of these interactions. However, when attempting to reconstruct the signaling networks and pathways between these sources and targets, one faces a substantial challenge. Although pathways are directed, high-throughput protein interaction data are undirected. In order to utilize the available data, we need methods that can orient protein interaction edges and discover high-confidence pathways that explain the observed experimental outcomes. We formalize the orientation problem in weighted protein interaction graphs as an optimization problem and present three approximation algori

SUBMITTER: Gitter A 

PROVIDER: S-EPMC3045580 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature