Computational verification of protein-protein interactions by orthologous co-expression.docVIP

BMC Bioinformatics BioMedCentral Methodology article Open Access Computational verification of protein-protein interactions by orthologous co-expression Itay Tirosh and Naama Barkai* Address: Departments of Molecular Genetics and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel Email: Itay Tirosh - itay.tirosh@weizmann.ac.il; Naama Barkai* - naama.barkai@weizmann.ac.il * Corresponding author Published: 02 March 2005 Received: 08 September 2004 Accepted: 02 March 2005 BMC Bioinformatics 2005, 6:40 doi:10.1186/1471-2105-6-40 This article is available from: /1471-2105/6/40 ? 2005 Tirosh and Barkai; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: High-throughput methods identify an overwhelming number of protein-protein interactions. However, the limited accuracy of these methods results in the false identification of many spurious interactions. Accordingly, the resulting interactions are regarded as hypothetical and computational methods are needed to increase their confidence. Several methods have recently been suggested for this purpose including co-expression as a confidence measure for interacting proteins, but their performance is still quite poor. Results: We introduce a novel computational method for verification of protein-protein interactions based on the co-expression of orthologs of interacting partners. The performance of our method is analysed using known S. cerevisiae interactions, and is shown to overcome limitations of previous methods. We present specific examples of known and putative interactions that are detected by our method and not by previous methods, and suggest that they represent transient interactions that