A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification

doi:10.1016/j.compbiolchem.2011.07.005

	A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification
	Yu, Liang 1; Gao, Lin 1; Li, Kui 1; Zhao, Yi 2; Chiu, David K. Y.3
	2011-10-12
发表期刊	COMPUTATIONAL BIOLOGY AND CHEMISTRY
ISSN	1476-9271
卷号	35 期号:5 页码:298-307
摘要	Since cellular functionality is typically envisioned as having a hierarchical structure, we propose a framework to identify modules (or clusters) within protein-protein interaction (PPI) networks in this paper. Based on the within-module and between-module edges of subgraphs and degree distribution, we present a formal module definition in PPI networks. Using the new module definition, an effective quantitative measure is introduced for the evaluation of the partition of PPI networks. Because of the hierarchical nature of functional modules, a hierarchical agglomerative clustering algorithm is developed based on the new measure in order to solve the problem of complexes detection within PPI networks. We use gold standard sets of protein complexes to validate the biological significance of predicted complexes. A comprehensive comparison is performed between our method and other four representative methods. The results show that our algorithm finds more protein complexes with high biological significance and a significant improvement. Furthermore, the predicted complexes by our method, whether dense or sparse, match well with known biological characteristics. (c) 2011 Elsevier Ltd. All rights reserved.
关键词	Protein-protein interaction (PPI) networks Complexes Degree distribution Hierarchical agglomerative algorithm
DOI	10.1016/j.compbiolchem.2011.07.005
收录类别	SCI
语种	英语
资助项目	National Key Natural Science Foundation of China[60933009] ; Specialized Research Fund for the Doctoral Program of Higher Education[200807010013] ; Fundamental Research Funds for the Central Universities[K50510030006] ; National Natural Science Foundation of China[61072103] ; Natural Sciences and Engineering Research Council of Canada
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Computer Science
WOS类目	Biology ; Computer Science, Interdisciplinary Applications
WOS记录号	WOS:000296930400005
出版者	ELSEVIER SCI LTD
引用统计	被引频次：6[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/12837
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Yu, Liang
作者单位	1.Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Peoples R China 2.Chinese Acad Sci, Bioinformat Grp, Inst Comp Technol, Beijing 100080, Peoples R China 3.Univ Guelph, Sch Comp Sci, Guelph, ON N1G 2W1, Canada
推荐引用方式 GB/T 7714	Yu, Liang,Gao, Lin,Li, Kui,et al. A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification[J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY,2011,35(5):298-307.
APA	Yu, Liang,Gao, Lin,Li, Kui,Zhao, Yi,&Chiu, David K. Y..(2011).A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification.COMPUTATIONAL BIOLOGY AND CHEMISTRY,35(5),298-307.
MLA	Yu, Liang,et al."A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification".COMPUTATIONAL BIOLOGY AND CHEMISTRY 35.5(2011):298-307.