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Ranking Candidate Disease Genes from Gene Expression and Protein Interaction: A Katz-Centrality Based Approach
Zhao, J; Yang, TH; Huang, YX; Holme, P; Zhao, J (reprint author), Logist Engn Univ, Dept Math, Chongqing, Peoples R China.
2011
发表期刊PLOS ONE
ISSN1932-6203
卷号6期号:9页码:e24306
摘要Many diseases have complex genetic causes, where a set of alleles can affect the propensity of getting the disease. The identification of such disease genes is important to understand the mechanistic and evolutionary aspects of pathogenesis, improve diagnosis and treatment of the disease, and aid in drug discovery. Current genetic studies typically identify chromosomal regions associated specific diseases. But picking out an unknown disease gene from hundreds of candidates located on the same genomic interval is still challenging. In this study, we propose an approach to prioritize candidate genes by integrating data of gene expression level, protein-protein interaction strength and known disease genes. Our method is based only on two, simple, biologically motivated assumptions-that a gene is a good disease-gene candidate if it is differentially expressed in cases and controls, or that it is close to other disease-gene candidates in its protein interaction network. We tested our method on 40 diseases in 58 gene expression datasets of the NCBI Gene Expression Omnibus database. On these datasets our method is able to predict unknown disease genes as well as identifying pleiotropic genes involved in the physiological cellular processes of many diseases. Our study not only provides an effective algorithm for prioritizing candidate disease genes but is also a way to discover phenotypic interdependency, cooccurrence and shared pathophysiology between different disorders.
部门归属[Zhao, Jing; Yang, Ting-Hong] Logist Engn Univ, Dept Math, Chongqing, Peoples R China; [Huang, Yongxu] Univ Pittsburgh, Dept Hlth Policy & Management, Pittsburgh, PA USA; [Holme, Petter] Umea Univ, Dept Phys, IceLab, Umea, Sweden; [Holme, Petter] Sungkyunkwan Univ, Dept Energy Sci, Suwon, South Korea; [Holme, Petter] Chinese Acad Sci, Kavli Inst Theoret Phys China, Beijing, Peoples R China
关键词Genome-wide Association Onset Alzheimer-disease Microarray Data Interaction Networks Identification Prioritization Polymorphism Pathology Model Risk
学科领域Physics
资助者National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029]
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收录类别SCI
语种英语
资助者National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029] ; National Natural Science Foundation of China [10971227]; Swedish Research Council; National Research Foundation of Korea; Ministry of Education, Science and Technology [R31-2008-10029]
WOS记录号WOS:000294686100033
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被引频次:27[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/14276
专题理论物理所SCI论文
通讯作者Zhao, J (reprint author), Logist Engn Univ, Dept Math, Chongqing, Peoples R China.
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Zhao, J,Yang, TH,Huang, YX,et al. Ranking Candidate Disease Genes from Gene Expression and Protein Interaction: A Katz-Centrality Based Approach[J]. PLOS ONE,2011,6(9):e24306.
APA Zhao, J,Yang, TH,Huang, YX,Holme, P,&Zhao, J .(2011).Ranking Candidate Disease Genes from Gene Expression and Protein Interaction: A Katz-Centrality Based Approach.PLOS ONE,6(9),e24306.
MLA Zhao, J,et al."Ranking Candidate Disease Genes from Gene Expression and Protein Interaction: A Katz-Centrality Based Approach".PLOS ONE 6.9(2011):e24306.
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