Graphical Features of Functional Genes in Human Protein Interaction Network

doi:10.1109/TBCAS.2015.2487299

CSpace > 系统科学研究所

	Graphical Features of Functional Genes in Human Protein Interaction Network
	Wang, Pei 1; Chen, Yao 2; Lu, Jinhu3 ; Wang, Qingyun 4; Yu, Xinghuo 5
	2016-06-01
发表期刊	IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS
ISSN	1932-4545
卷号	10 期号:3 页码:707-720
摘要	With the completion of the human genome project, it is feasible to investigate large-scale human protein interaction network (HPIN) with complex networks theory. Proteins are encoded by genes. Essential, viable, disease, conserved, housekeeping (HK) and tissue-enriched (TE) genes are functional genes, which are organized and functioned via interaction networks. Based on up-to-date data from various databases or literature, two large-scale HPINs and six subnetworks are constructed. We illustrate that the HPINs and most of the subnetworks are sparse, small-world, scale-free, disassortative and with hierarchical modularity. Among the six subnetworks, essential, disease and HK subnetworks are more densely connected than the others. Statistical analysis on the topological structures of the HPIN reveals that the lethal, the conserved, the HK and the TE genes are with hallmark graphical features. Receiver operating characteristic (ROC) curves indicate that the essential genes can be distinguished from the viable ones with accuracy as high as almost 70%. Closeness, semi-local and eigenvector centralities can distinguish the HK genes from the TE ones with accuracy around 82%. Furthermore, the Venn diagram, cluster dendgrams and classifications of disease genes reveal that some classes of disease genes are with hallmark graphical features, especially for cancer genes, HK disease genes and TE disease genes. The findings facilitate the identification of some functional genes via topological structures. The investigations shed some light on the characteristics of the compete interactome, which have potential implications in networked medicine and biological network control.
关键词	Cluster disease classification functional gene human protein interaction network receiver operating characteristic (ROC) curve topological structure
DOI	10.1109/TBCAS.2015.2487299
语种	英语
资助项目	National Science and Technology Major Project of China[2014ZX10004-001-014] ; National Natural Science Foundation of China[61304151] ; National Natural Science Foundation of China[61532020] ; National Natural Science Foundation of China[11472290] ; National Natural Science Foundation of China[11172215] ; National Natural Science Foundation of China[61174028] ; Australia ARC Discovery Grant[DP130104765]
WOS研究方向	Engineering
WOS类目	Engineering, Biomedical ; Engineering, Electrical & Electronic
WOS记录号	WOS:000381440400016
出版者	IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/23520
专题	系统科学研究所
通讯作者	Wang, Pei
作者单位	1.Henan Univ, Sch Math & Stat, Kaifeng 475004, Peoples R China 2.Hong Kong Polytech Univ, Dept Comp, Hong Kong, Hong Kong, Peoples R China 3.Chinese Acad Sci, Inst Syst Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 4.Beihang Univ, Dept Dynam & Control, Beijing 100191, Peoples R China 5.RMIT Univ, Sch Elect & Comp Engn, Melbourne, Vic 3001, Australia
推荐引用方式 GB/T 7714	Wang, Pei,Chen, Yao,Lu, Jinhu,et al. Graphical Features of Functional Genes in Human Protein Interaction Network[J]. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS,2016,10(3):707-720.
APA	Wang, Pei,Chen, Yao,Lu, Jinhu,Wang, Qingyun,&Yu, Xinghuo.(2016).Graphical Features of Functional Genes in Human Protein Interaction Network.IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS,10(3),707-720.
MLA	Wang, Pei,et al."Graphical Features of Functional Genes in Human Protein Interaction Network".IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 10.3(2016):707-720.