Topological structure analysis of the protein-protein interaction network in budding yeast |
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| Authors: | Bu Dongbo Zhao Yi Cai Lun Xue Hong Zhu Xiaopeng Lu Hongchao Zhang Jingfen Sun Shiwei Ling Lunjiang Zhang Nan Li Guojie Chen Runsheng |
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| Affiliation: | Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. |
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| 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. |
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