The Comparative Genomics of Protein Interactions

José M. Peregrín-Alvarez[1],[2] (
Christos A. Ouzounis[3] (

[1]Sick Kids Research Institute, TMDT MARS Building, 101 College St., 15th Floor, East Tower, M5G 1L7 Toronto, ON, Canada
[2]Dpt. Of Molecular Biology and Biochemistry, University of Malaga, 29071 Malaga, Spain
[3]Institute of Agrobiotechnology, Hellas 6th Km Charilaou, Thermi Rd, P.O. Box 361, 570 01 Thermi, Thessaloniki, Greece


The detection of gene fusion events across genomes can be used for the prediction of functional associations of proteins, including physical interactions or complex formation. These predictions are obtained by the detection of similarity for pairs of ‘component’ proteins to ‘composite’ proteins. Since the amount of composite proteins is limited in nature, we augment this set by creating artificial fusion proteins from experimentally determined protein interacting pairs. The goal is to study the extent of protein interaction partners with increasing phylogenetic distance, using an automated method. We have thus detected component pairs within seven entire genome sequences of similar size, using artificially generated composite proteins that have been shown to interact experimentally. Our results indicate that protein interactions are not conserved over large phylogenetic distances. In addition, we provide a set of predictions for functionally associated proteins across seven species using experimental information and demonstrate the applicability of fusion analysis for the comparative genomics of protein interactions.

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Japanese Society for Bioinformatics