Title: A technique to search for functional similarities in protein-protein interaction networks

Authors: Valeria Fionda, Luigi Palopoli, Simona Panni, Simona E. Rombo

Addresses: Department of Mathematics, University of Calabria, Via P. Bucci, Rende (CS), Italy. ' Department of Electronics, Computer Science and Systems, University of Calabria, Via P. Bucci, Rende (CS), Italy. ' Department of Cellular Biology, University of Calabria, Via P. Bucci, Rende (CS), Italy. ' Department of Electronics, Computer Science and Systems, University of Calabria, Via P. Bucci, Rende (CS), Italy

Abstract: We describe a method to search for similarities across protein-protein interaction networks of different organisms. The technique core consists in computing a maximum weight matching of bipartite graphs resulting from comparing the neighbourhoods of proteins belonging to different networks. Both quantitative and reliability information are exploited. We tested the method on the networks of S. cerevisiae, D. melanogaster and C. elegans. The experiments showed that the technique is able to detect functional orthologs when the sole sequence similarity does not prove itself sufficient. They also demonstrated the capability of our approach in discovering common biological processes involving uncharacterised proteins.

Keywords: biological networks alignment; PPI networks comparison; functional orthologs detection; bipartite graph weighted matching; functional similarities; protein-protein interaction; common processes; biological processes; uncharacterised proteins.

DOI: 10.1504/IJDMB.2009.029205

International Journal of Data Mining and Bioinformatics, 2009 Vol.3 No.4, pp.431 - 453

Available online: 09 Nov 2009

Full-text access for editors Access for subscribers Purchase this article Comment on this article