Journal Article

Domain-oriented edge-based alignment of protein interaction networks

Xin Guo and Alexander J. Hartemink

in Bioinformatics

Volume 25, issue 12, pages i240-1246
Published in print June 2009 | ISSN: 1367-4803
Published online May 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp202

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Motivation: Recent advances in high-throughput experimental techniques have yielded a large amount of data on protein–protein interactions (PPIs). Since these interactions can be organized into networks, and since separate PPI networks can be constructed for different species, a natural research direction is the comparative analysis of such networks across species in order to detect conserved functional modules. This is the task of network alignment.

Results: Most conventional network alignment algorithms adopt a node-then-edge-alignment paradigm: they first identify homologous proteins across networks and then consider interactions among them to construct network alignments. In this study, we propose an alternative direct-edge-alignment paradigm. Specifically, instead of explicit identification of homologous proteins, we directly infer plausibly alignable PPIs across species by comparing conservation of their constituent domain interactions. We apply our approach to detect conserved protein complexes in yeast–fly and yeast–worm PPI networks, and show that our approach outperforms two recent approaches in most alignment performance metrics.

Availability: Supplementary material and source code can be found at http://www.cs.duke.edu/∼amink/.

Contact: xinguo@cs.duke.edu

Journal Article.  4541 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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