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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
发表期刊NUCLEIC ACIDS RESEARCH
ISSN0305-1048
文章类型Article
卷号39页码:W437-W443
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摘要Genome-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/.
学科领域Physiological Psychology/biological Psychology
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收录类别SCI
语种英语
项目资助者Chinese Academy of Sciences [KSCX2-EW-J-8] ; Institute of Psychology, Chinese Academy of Sciences [O9CX115011]
项目简介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记录号WOS:000292325300071
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被引频次:47[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.psych.ac.cn/handle/311026/12847
专题中国科学院心理健康重点实验室
通讯作者Wang, J (reprint author), Chinese Acad Sci, Inst Psychol, Key Lab Mental Hlth, Beijing 100101, Peoples R China.
作者单位1.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
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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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