QNet: A tool for querying protein interaction networks

Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafha, Roded Sharan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Molecular interaction databases can be used to study the evolution of molecular pathways across species. Querying such pathways is a challenging computational problem, and recent efforts have been limited to simple queries (paths), or simple networks (forests). In this paper, we significantly extend the class of pathways that can be efficiently queried to the case of trees, and graphs of bounded treewidth. Our algorithm allows the identification of non-exact (homeomorphic) matches, exploiting the color coding technique of Alon et al. We implement a tool for tree queries, called QNet, and test its retrieval properties in simulations and on real network data. We show that QNet searches queries with up to 9 proteins in seconds on current networks, and outperforms sequence-based searches. We also use QNet to perform the first large scale cross-species comparison of protein complexes, by querying known yeast complexes against a fly protein interaction network. This comparison points to strong conservation between the two species, and underscores the importance of our tool in mining protein interaction networks.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 11th Annual International Conference, RECOMB 2007, Proceedings
PublisherSpringer Verlag
Pages1-15
Number of pages15
ISBN (Print)3540716807, 9783540716808
DOIs
StatePublished - 2007
Event11th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2007 - Oakland, CA, United States
Duration: 21 Apr 200725 Apr 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4453 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference11th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2007
Country/TerritoryUnited States
CityOakland, CA
Period21/04/0725/04/07

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