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ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework
Zhang, Kunlin1; Chang, Suhua1,2; Cui, Sijia1,2; Guo, Liyuan1; Zhang, Liuyan1,2; Wang, Jing1; Wang, J (reprint author), Chinese Acad Sci, Inst Psychol, Key Lab Mental Hlth, Beijing 100101, Peoples R China.
2011-07-01
Source PublicationNUCLEIC ACIDS RESEARCH
ISSN0305-1048
SubtypeArticle
Volume39Pages:W437-W443
Contribution Rank1
AbstractGenome-wide association study (GWAS) is widely utilized to identify genes involved in human complex disease or some other trait. One key challenge for GWAS data interpretation is to identify causal SNPs and provide profound evidence on how they affect the trait. Currently, researches are focusing on identification of candidate causal variants from the most significant SNPs of GWAS, while there is lack of support on biological mechanisms as represented by pathways. Although pathway-based analysis (PBA) has been designed to identify disease-related pathways by analyzing the full list of SNPs from GWAS, it does not emphasize on interpreting causal SNPs. To our knowledge, so far there is no web server available to solve the challenge for GWAS data interpretation within one analytical framework. ICSNPathway is developed to identify candidate causal SNPs and their corresponding candidate causal pathways from GWAS by integrating linkage disequilibrium (LD) analysis, functional SNP annotation and PBA. ICSNPathway provides a feasible solution to bridge the gap between GWAS and disease mechanism study by generating hypothesis of SNP gene pathway(s). The ICSNPathway server is freely available at http://icsnpathway.psych.ac.cn/.
Subject AreaPhysiological Psychology/biological Psychology
URL查看原文
Indexed BySCI
Language英语
Funding OrganizationChinese Academy of Sciences [KSCX2-EW-J-8] ; Institute of Psychology, Chinese Academy of Sciences [O9CX115011]
Project Intro.Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-J-8); Project for Young Scientists Fund, Institute of Psychology, Chinese Academy of Sciences (O9CX115011). Funding for open access charge: KSCX2-EW-J-8.
WOS IDWOS:000292325300071
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Cited Times:52[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.psych.ac.cn/handle/311026/12847
Collection中国科学院心理健康重点实验室
Corresponding AuthorWang, J (reprint author), Chinese Acad Sci, Inst Psychol, Key Lab Mental Hlth, Beijing 100101, Peoples R China.
Affiliation1.Chinese Acad Sci, Inst Psychol, Key Lab Mental Hlth, Beijing 100101, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
First Author AffilicationKey Laboratory of Mental Health, CAS
Recommended Citation
GB/T 7714
Zhang, Kunlin,Chang, Suhua,Cui, Sijia,et al. ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework[J]. NUCLEIC ACIDS RESEARCH,2011,39:W437-W443.
APA Zhang, Kunlin.,Chang, Suhua.,Cui, Sijia.,Guo, Liyuan.,Zhang, Liuyan.,...&Wang, J .(2011).ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.NUCLEIC ACIDS RESEARCH,39,W437-W443.
MLA Zhang, Kunlin,et al."ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework".NUCLEIC ACIDS RESEARCH 39(2011):W437-W443.
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