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Nucleic Acids Res. 2003 May 1;31(9):2443-50.

Topological structure analysis of the protein-protein interaction network in budding yeast.

Author information

  • 1Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.

Abstract

Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques and quasi-bipartites) of complicated protein-protein interaction networks. Our analyses suggest that these hidden topological structures consist of biologically relevant functional groups. This result motivates a new method to predict the function of uncharacterized proteins based on the classification of known proteins within topological structures. Using this spectral analysis method, 48 quasi-cliques and six quasi-bipartites were isolated from a network involving 11,855 interactions among 2617 proteins in budding yeast, and 76 uncharacterized proteins were assigned functions.

PMID:
12711690
[PubMed - indexed for MEDLINE]
PMCID:
PMC154226
Free PMC Article

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