QPath: a method for querying pathways in a protein-protein interaction network

Background: Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks. Results: We present a comprehensive framework for protein network searches using pathway queries. Given a linear query pathway and a network of interest, our algorithm, QPath, efficiently searches the network for homologous pathways, allowing both insertions and deletions of proteins in the identified pathways. Matched pathways are automatically scored according to their variation from the query pathway in terms of the protein insertions and deletions they employ, the sequence similarity of their constituent proteins to the query proteins, and the reliability of their constituent interactions. We applied QPath to systematically infer protein pathways in fly...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Tomer Shlomi, Daniel Segal, Eytan Ruppin, Roded Sharan
• Keywords: BMCBI 2006, Protein, Protein Network, Query Pathways