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