Exploring hierarchical and overlapping modular structure in the yeast protein interaction network

doi:10.1186/1471-2164-11-S4-S17

	Exploring hierarchical and overlapping modular structure in the yeast protein interaction network
	Liu, Changning; Li, Jing; Zhao, Yi
	2010-12-02
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	11 页码:12
摘要	Background: Developing effective strategies to reveal modular structures in protein interaction networks is crucial for better understanding of molecular mechanisms of underlying biological processes. In this paper, we propose a new density-based algorithm (ADHOC) for clustering vertices of a protein interaction network using a novel subgraph density measurement. Results: By statistically evaluating several independent criteria, we found that ADHOC could significantly improve the outcome as compared with five previously reported density-dependent methods. We further applied ADHOC to investigate the hierarchical and overlapping modular structure in the yeast PPI network. Our method could effectively detect both protein modules and the overlaps between them, and thus greatly promote the precise prediction of protein functions. Moreover, by further assaying the intermodule layer of the yeast PPI network, we classified hubs into two types, module hubs and inter-module hubs. Each type presents distinct characteristics both in network topology and biological functions, which could conduce to the better understanding of relationship between network architecture and biological implications. Conclusions: Our proposed algorithm based on the novel subgraph density measurement makes it possible to more precisely detect hierarchical and overlapping modular structures in protein interaction networks. In addition, our method also shows a strong robustness against the noise in network, which is quite critical for analyzing such a high noise network.
DOI	10.1186/1471-2164-11-S4-S17
收录类别	SCI
语种	英语
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000289200700017
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：11[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/2XEOYT63/12030
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Liu, Changning
作者单位	Chinese Acad Sci, Inst Comp Technol, Ctr Adv Comp Res, Bioinformat Grp,Key Lab Intelligent Informat Proc, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Liu, Changning,Li, Jing,Zhao, Yi. Exploring hierarchical and overlapping modular structure in the yeast protein interaction network[J]. BMC GENOMICS,2010,11:12.
APA	Liu, Changning,Li, Jing,&Zhao, Yi.(2010).Exploring hierarchical and overlapping modular structure in the yeast protein interaction network.BMC GENOMICS,11,12.
MLA	Liu, Changning,et al."Exploring hierarchical and overlapping modular structure in the yeast protein interaction network".BMC GENOMICS 11(2010):12.