ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework

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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
刊名	NUCLEIC ACIDS RESEARCH
	2011-07-01
卷号	39 页码:W437-W443
ISSN号	0305-1048
通讯作者	Wang, J (reprint author), Chinese Acad Sci, Inst Psychol, Key Lab Mental Hlth, Beijing 100101, Peoples R China.
产权排序	1
英文摘要	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/.
学科主题	Physiological psychology/Biological Psychology
收录类别	SCI
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.
原文出处	http://nar.oxfordjournals.org/content/early/2011/05/27/nar.gkr391.full-text-lowres.pdf
语种	英语
WOS记录号	WOS:000292325300071
内容类型	期刊论文
源URL	[http://ir.psych.ac.cn/handle/311026/12847]
专题	心理研究所_中国科学院心理健康重点实验室
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
推荐引用方式 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, Jing.(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.