Determining modular organization of protein interaction networks by maximizing modularity density

doi:10.1186/1752-0509-4-S2-S10

CSpace > 应用数学研究所

	Determining modular organization of protein interaction networks by maximizing modularity density
	Zhang, Shihua1 ; Ning, Xue-Mei 2; Ding, Chris 3; Zhang, Xiang-Sun
	2010-09-13
发表期刊	BMC SYSTEMS BIOLOGY
ISSN	1752-0509
卷号	4 页码:12
摘要	Background: With ever increasing amount of available data on biological networks, modeling and understanding the structure of these large networks is an important problem with profound biological implications. Cellular functions and biochemical events are coordinately carried out by groups of proteins interacting each other in biological modules. Identifying of such modules in protein interaction networks is very important for understanding the structure and function of these fundamental cellular networks. Therefore, developing an effective computational method to uncover biological modules should be highly challenging and indispensable. Results: The purpose of this study is to introduce a new quantitative measure modularity density into the field of biomolecular networks and develop new algorithms for detecting functional modules in protein-protein interaction (PPI) networks. Specifically, we adopt the simulated annealing (SA) to maximize the modularity density and evaluate its efficiency on simulated networks. In order to address the computational complexity of SA procedure, we devise a spectral method for optimizing the index and apply it to a yeast PPI network. Conclusions: Our analysis of detected modules by the present method suggests that most of these modules have well biological significance in context of protein complexes. Comparison with the MCL and the modularity based methods shows the efficiency of our method.
DOI	10.1186/1752-0509-4-S2-S10
语种	英语
WOS研究方向	Mathematical & Computational Biology
WOS类目	Mathematical & Computational Biology
WOS记录号	WOS:000208294800009
出版者	BIOMED CENTRAL LTD
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/231
专题	应用数学研究所
通讯作者	Zhang, Shihua
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, Peoples R China 2.Beijing Forestry Univ, Coll Sci, Beijing 100083, Peoples R China 3.Univ Texas Arlington, Dept Comp Sci & Engn, Arlington, TX 76019 USA
推荐引用方式 GB/T 7714	Zhang, Shihua,Ning, Xue-Mei,Ding, Chris,et al. Determining modular organization of protein interaction networks by maximizing modularity density[J]. BMC SYSTEMS BIOLOGY,2010,4:12.
APA	Zhang, Shihua,Ning, Xue-Mei,Ding, Chris,&Zhang, Xiang-Sun.(2010).Determining modular organization of protein interaction networks by maximizing modularity density.BMC SYSTEMS BIOLOGY,4,12.
MLA	Zhang, Shihua,et al."Determining modular organization of protein interaction networks by maximizing modularity density".BMC SYSTEMS BIOLOGY 4(2010):12.