title: Topological structure analysis of the protein-protein interaction network in budding yeast.
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.
authors.affiliation: Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
authors.forename: Lun
authors.initials: L
authors.lastname: Cai
authors.forename: Hong
authors.initials: H
authors.lastname: Xue
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Hongchao
authors.initials: H
authors.lastname: Lu
authors.forename: Jingfen
authors.initials: J
authors.lastname: Zhang
authors.forename: Shiwei
authors.initials: S
authors.lastname: Sun
authors.forename: Lunjiang
authors.initials: L
authors.lastname: Ling
authors.forename: Nan
authors.initials: N
authors.lastname: Zhang
authors.forename: Guojie
authors.initials: G
authors.lastname: Li
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D008954:Models, Biological; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D004718:Saccharomycetales / Q000378:metabolism*
chemical_list: D011506:Proteins