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Nucleic Acids Research, 2003, Vol. 31, No. 9 2443-2450
© 2003 Oxford University Press

Topological structure analysis of the protein–protein interaction network in budding yeast

Dongbo Bu1, Yi Zhao1, Lun Cai1, Hong Xue2, Xiaopeng Zhu2, Hongchao Lu1, Jingfen Zhang1, Shiwei Sun1, Lunjiang Ling2, Nan Zhang2, Guojie Li1 and Runsheng Chen1,2

1 Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology and 2 Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

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.


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