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Open Access Methodology article

Clustering proteins from interaction networks for the prediction of cellular functions

Christine Brun1, Carl Herrmann1* and Alain Guénoche2

Author Affiliations

1 Laboratoire de Génétique et Physiologie du Développement, IBDM, CNRS/INSERM/Université de la Méditerranée

2 lnstitut de Mathématiques de Luminy CNRS Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 9, France

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BMC Bioinformatics 2004, 5:95  doi:10.1186/1471-2105-5-95

Published: 13 July 2004



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.


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.


We believe that our results represent a significant improvement for the inference of cellular functions, that can be applied to other organism as well as to other type of interaction graph, such as genetic interactions.