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Bioinformatics Advance Access originally published online on May 19, 2005
Bioinformatics 2005 21(15):3279-3285; doi:10.1093/bioinformatics/bti492
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Inferring protein–protein interactions through high-throughput interaction data from diverse organisms

Yin Liu 1, Nianjun Liu 2 and Hongyu Zhao 2,3,*

1Program of Computational Biology and Bioinformatics, Yale University New Haven, CT 06520, USA
2Department of Epidemiology and Public Health, Yale University School of Medicine New Haven, CT 06520, USA
3Department of Genetics, Yale University School of Medicine New Haven, CT 06520, USA

*To whom correspondence should be addressed.

Motivation: Identifying protein–protein interactions is critical for understanding cellular processes. Because protein domains represent binding modules and are responsible for the interactions between proteins, computational approaches have been proposed to predict protein interactions at the domain level. The fact that protein domains are likely evolutionarily conserved allows us to pool information from data across multiple organisms for the inference of domain–domain and protein–protein interaction probabilities.

Results: We use a likelihood approach to estimating domain–domain interaction probabilities by integrating large-scale protein interaction data from three organisms, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. The estimated domain–domain interaction probabilities are then used to predict protein–protein interactions in S.cerevisiae. Based on a thorough comparison of sensitivity and specificity, Gene Ontology term enrichment and gene expression profiles, we have demonstrated that it may be far more informative to predict protein–protein interactions from diverse organisms than from a single organism.

Availability: The program for computing the protein–protein interaction probabilities and supplementary material are available at http://bioinformatics.med.yale.edu/interaction

Contact: hongyu.zhao{at}yale.edu

Received on March 2, 2005; revised on April 14, 2005; accepted on May 6, 2005

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