Abstract
Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. After that, the functional annotation and enrichment analysis of significant SNPs are important tasks. Classic methods are always based on physical positions of SNPs and genes. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in gene expression levels and have been proven efficient to connect SNPs and genes. In this work, we integrated the eQTL data and Gene Ontology (GO), constructed associations between SNPs and GO terms, then performed functional enrichment analysis. Finally, we constructed an eQTL-based SNP Ontology and SNP functional enrichment analysis platform. Taking Parkinson Disease (PD) as an example, the proposed platform and method are efficient. We believe eSNPO will be a useful resource for SNP functional annotation and enrichment analysis after we have got significant disease related SNPs.
Highlights
Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases
Genome-wide association study (GWAS) is an examination of many common genetic variants in different individuals to see if any variant is associated with a trait
Since two single nucleotide polymorphisms (SNPs) with significantly altered allele frequency between the Age-related Macular Degeneration (ARMD) and healthy controls was firstly found in 20052, more than 100,000 risk SNPs associated to hundreds of diseases in human have been mined via GWAS3
Summary
Jin Li1,2,3,*, Limei Wang4,5,*, Tao Jiang[1], Jizhe Wang[1], Xue Li1, Xiaoyan Liu[2], Chunyu Wang[2], Zhixia Teng[2], Ruijie Zhang[1], Hongchao Lv1 & Maozu Guo[2]. Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. The functional annotation and enrichment analysis of significant SNPs are important tasks. We integrated the eQTL data and Gene Ontology (GO), constructed associations between SNPs and GO terms, performed functional enrichment analysis. We believe eSNPO will be a useful resource for SNP functional annotation and enrichment analysis after we have got significant disease related. GWAS studies typically focus on associations between single nucleotide polymorphisms (SNPs) and traits like major complex diseases[1]. A common ground in these methods is that the SNP functions are explained by the related genes according to physical positions on chromosome.
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