Topology-free querying of protein interaction networks

Sharon Bruckner*, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan

*Corresponding author for this work

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


In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction network of species B; the goal is to identify subnetworks of B that are similar to the query. Existing approaches mostly depend on knowledge of the interaction topology of the query in the network of species A; however, in practice, this topology is often not known. To combat this problem, we develop a topology-free querying algorithm, which we call Torque. Given a query, represented as a set of proteins, Torque seeks a matching set of proteins that are sequence-similar to the query proteins and span a connected region of the network, while allowing both insertions and deletions. The algorithm uses alternatively dynamic programming and integer linear programming for the search task. We test Torque with queries from yeast, fly, and human, where we compare it to the QNet topology-based approach, and with queries from less studied species, where only topology-free algorithms apply. Torque detects many more matches than QNet, while in both cases giving results that are highly functionally coherent.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings
Number of pages16
StatePublished - 2009
Event13th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2009 - Tucson, AZ, United States
Duration: 18 May 200921 May 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5541 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference13th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2009
Country/TerritoryUnited States
CityTucson, AZ


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