title: ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.
abstract: 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/.
authors.affiliation: Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Kunlin
authors.initials: K
authors.lastname: Zhang
authors.forename: Suhua
authors.initials: S
authors.lastname: Chang
authors.forename: Sijia
authors.initials: S
authors.lastname: Cui
authors.forename: Liyuan
authors.initials: L
authors.lastname: Guo
authors.forename: Liuyan
authors.initials: L
authors.lastname: Zhang
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
mesh_terms: D001172:Arthritis, Rheumatoid / Q000235:genetics; D055106:Genome-Wide Association Study; D006801:Humans; D020407:Internet; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012984:Software