1
Department of Physics, University of Notre
Dame, Notre Dame, Indiana 46556,
USA.
2
International School for Advanced Studies (SISSA)
and INFM, V. Beirut 2-4, 34014 Trieste,
Italy.
3
The Abdus Salam International Centre for
Theoretical Physics, P.O. Box 586, 34100 Trieste,
Italy.
4
Laboratoire de Physique Théorique (UMR du
CNRS 8627), Bâtiment 210 Université de Paris-Sud
91405 Orsay Cedex, France.
Correspondence should be addressed to Alexei Vazquez avazque1@nd.edu
Determining protein function is one of the most challenging problems
of the post-genomic era. The availability of entire genome sequences and of
high-throughput capabilities to determine gene coexpression patterns has
shifted the research focus from the study of single proteins or small complexes
to that of the entire proteome1. In this context, the search for
reliable methods for assigning protein function is of primary importance. There
are various approaches available for deducing the function of proteins of
unknown function using information derived from sequence similarity or
clustering patterns of co-regulated genes2,
3, phylogenetic
profiles4, protein-protein interactions (refs.
5−8 and Samanta, M.P. and Liang, S.,
unpublished data), and protein complexes9,
10. Here we propose
the assignment of proteins to functional classes on the basis of their network
of physical interactions as determined by minimizing the number of protein
interactions among different functional categories. Function assignment is
proteome-wide and is determined by the global connectivity pattern of the
protein network. The approach results in multiple functional assignments, a
consequence of the existence of multiple equivalent solutions. We apply the
method to analyze the yeast Saccharomyces cerevisiae protein-protein
interaction network5. The robustness of the approach is tested in
a system containing a high percentage of unclassified proteins and also in
cases of deletion and insertion of specific protein interactions.
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