Clustering proteins from interaction networks for the prediction of cellular functions.docVIP

BMC Bioinformatics BioMedCentral Methodology article Open Access Clustering proteins from interaction networks for the prediction of cellular functions Christine Brun1, Carl Herrmann*1 and Alain Guénoche2 Address: 1Laboratoire de Génétique et Physiologie du Développement, IBDM, CNRS/INSERM/Université de la Méditerranée and 2lnstitut de Mathématiques de Luminy CNRS Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 9, France Email: Christine Brun - brun@ibdm.univ-mrs.fr; Carl Herrmann* - herrmann@ibdm.univ-mrs.fr; Alain Guénoche - guenoche@rs-mrs.fr * Corresponding author Published: 13 July 2004 Received: 29 March 2004 Accepted: 13 July 2004 BMC Bioinformatics 2004, 5:95 doi:10.1186/1471-2105-5-95 This article is available from: /1471-2105/5/95 ? 2004 Brun et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the articles original URL. Abstract Background: Developing reliable and efficient strategies allowing to infer a function to yet uncharacterized proteins based on interaction networks is of crucial interest in the current context of high-throughput data generation. In this paper, we develop a new algorithm for clustering vertices of a protein-protein interaction network using a density function, providing disjoint classes. Results: Applied to the yeast interaction network, the classes obtained appear to be biological significant. The partitions are then used to make functional predictions for uncharacterized yeast proteins, using an annotation procedure that takes into account the binary interactions between proteins inside the classes. We show that this procedure is able to enhance the performances with respect to previous approaches. Finally, we propose a new annotation for 37 previously uncharacterized yeast proteins. Conclusio