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An Effective Link-Based Clustering Algorithm for Detecting Overlapping Protein Complexes in Protein-Protein Interaction Networks

文献类型：期刊论文

作者Hu, Lun1,2; Zhang, Jun3; Pan, Xiangyu3; Luo, Xin1,4,5; Yuan, Huaqiang1
刊名IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING
出版日期2021-10-01
卷号8期号:4页码:3275-3289
关键词Proteins Clustering algorithms Biology Search problems Partitioning algorithms Optimization Protein complex detection protein-protein interaction network link-based clustering network clustering
ISSN号2327-4697
DOI10.1109/TNSE.2021.3109880
通讯作者Luo, Xin(luoxin21@cigit.ac.cn) ; Yuan, Huaqiang(yuanhq@dgut.edu.cn)
英文摘要Protein complexes are one most important kind of functional modules for biological processes in cells. In this regard, their detection is vital for understanding the principle of cell organization and function. A variety of clustering algorithms have been developed to detect protein complexes from protein-protein interaction (PPI) networks. However, most of them are based on a certain clustering criterion. Given the fact that proteins should interact with each other rather than act independently, we reason that clustering upon interactions can better characterize protein complexes than upon proteins, thus improving the detection accuracy. To this end, a link-based clustering algorithm has been proposed in this paper to effectively detect overlapping protein complexes. It first measures the similarity between pairwise interactions from the perspectives of network topology and Gene Ontology. The problem of protein complex detection is then formulated as an optimization problem of link-based clustering, which is resolved by the proposed algorithm. This proposed algorithm explores the intrinsic correlation between protein complexes and interactions for detecting functionally significant protein complexes. Experimental results on five independent PPI datasets collected from the species of yeast and human demonstrate that compared with state-of-the-art algorithms, the proposed algorithm has significantly improved the detection accuracy for protein complexes.
资助项目Natural Science Foundation of Xinjiang Uygur Autonomous Region[2021D01D05] ; National Natural Science Foundation of China[61602352] ; Pioneer Hundred Talents Program of Chinese Academy of Sciences ; CAAI-Huawei MindSpore Open Fund[CAAIXSJLJJ-2020-004B] ; Chongqing Research Program of Technology Innovation and Application[cstc2019jscx-fxydX0027]
WOS研究方向Engineering ; Mathematics
语种英语
WOS记录号WOS:000728929300045
出版者IEEE COMPUTER SOC
源URL[http://119.78.100.138/handle/2HOD01W0/14731]  
专题中国科学院重庆绿色智能技术研究院
通讯作者Luo, Xin; Yuan, Huaqiang
作者单位1.Dongguan Univ Technol, Sch Comp Sci & Technol, Dongguan 523808, Peoples R China
2.Chinese Acad Sci, Tech Inst Phys & Chem, Urumqi 830011, Peoples R China
3.Wuhan Univ Technol, Sch Comp Sci & Technol, Wuhan 430070, Peoples R China
4.Chinese Acad Sci, Chongqing Engn Res Ctr Big Data Applicat Smart Ci, Chongqing 400714, Peoples R China
5.Chinese Acad Sci, Chongqing Key Lab Big Data & Intelligent Comp, Chongqing Inst Green & Intelligent Technol, Chongqing 400714, Peoples R China
推荐引用方式
GB/T 7714		 Hu, Lun,Zhang, Jun,Pan, Xiangyu,et al. An Effective Link-Based Clustering Algorithm for Detecting Overlapping Protein Complexes in Protein-Protein Interaction Networks[J]. IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING,2021,8(4):3275-3289.
APA Hu, Lun,Zhang, Jun,Pan, Xiangyu,Luo, Xin,&Yuan, Huaqiang.(2021).An Effective Link-Based Clustering Algorithm for Detecting Overlapping Protein Complexes in Protein-Protein Interaction Networks.IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING,8(4),3275-3289.
MLA Hu, Lun,et al."An Effective Link-Based Clustering Algorithm for Detecting Overlapping Protein Complexes in Protein-Protein Interaction Networks".IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING 8.4(2021):3275-3289.

入库方式： OAI收割

来源：重庆绿色智能技术研究院

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