QNet: a tool for querying protein interaction networks

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Banu DostRoded Sharan

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. (1995). 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 nine 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.

References

Dec 11, 1999·Nucleic Acids Research·I XenariosD Eisenberg
Jun 8, 2001·Annual Review of Biochemistry·M MannA Pandey
Aug 30, 2003·Oncogene·Paul DentSteven Grant
Sep 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Brian P KelleyTrey Ideker
Dec 19, 2003·Nucleic Acids Research·Minoru KanehisaMasahiro Hattori
Dec 4, 2004·Genome Biology·Clement A StanyonRussell L Finley
Jun 30, 2005·Bioinformatics·Ron Y PinterMichal Ziv-Ukelson
Dec 31, 2005·Nucleic Acids Research·H W MewesV Stümpflen
Dec 31, 2005·Nucleic Acids Research·Ulrich GüldenerVolker Stümpflen
Apr 12, 2006·BMC Bioinformatics·Tomer ShlomiRoded Sharan

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Citations

Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xiaoning QianByung-Jun Yoon
Aug 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jason FlannickSerafim Batzoglou
Mar 23, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Valeria Fionda, Luigi Palopoli
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sharon BrucknerRoded Sharan
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ferhat AyTamer Kahveci
Jun 21, 2011·Bioinformatics·Günhan Gülsoy, Tamer Kahveci
Jun 21, 2011·Bioinformatics·Phuong DaoS Cenk Sahinalp
Sep 20, 2011·Bioinformatics·Qiang HuangXiang-Sun Zhang
Jun 26, 2012·Bioinformatics·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Feb 16, 2013·Bioinformatics·Ahmet E Aladag, Cesim Erten
Jun 6, 2009·Nucleic Acids Research·Sharon BrucknerRoded Sharan
Aug 23, 2012·PloS One·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Feb 11, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mu-Fen Hsieh, Sing-Hoi Sze
Mar 10, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ilan SmolyMichal Ziv-Ukelson
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Mehmet Koyutürk
Feb 2, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Nadja BetzlerRolf Niedermeier
Oct 11, 2015·BMC Bioinformatics·Md Mahmudul Hasan, Tamer Kahveci
Feb 25, 2015·BMC Systems Biology·Hyundoo Jeong, Byung-Jun Yoon
Sep 20, 2008·Genome Biology·Eric BanksMona Singh
Apr 27, 2016·BMC Bioinformatics·Bhusan K KuntalSharmila S Mande
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Günhan GülsoyTamer Kahveci
Apr 20, 2010·Journal of Bioinformatics and Computational Biology·Misael MongiovìRoded Sharan
Apr 23, 2013·Journal of Bioinformatics and Computational Biology·Sriganesh Srihari, Hon Wai Leong
Jan 4, 2018·BMC Bioinformatics·Hyundoo JeongByung-Jun Yoon
May 7, 2020·Journal of the Royal Society, Interface·Deisy Morselli Gysi, Katja Nowick
Apr 20, 2018·BMC Systems Biology·Kingshuk MukherjeeTamer Kahveci
Oct 10, 2020·Computational and Structural Biotechnology Journal·Cheng-Yu Ma, Chung-Shou Liao

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