eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform.

Journal: Scientific reports
Published Date: Jul 29, 2016

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.

Authors

  • Jin Li
    Mental Health Center, West China Hospital, Sichuan University, Chengdu, China.
  • Limei Wang
    Institute of Intelligent System and Bioinformatics, College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China.
  • Tao Jiang
    Department of Respiratory and Critical Care Medicine, Center for Respiratory Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
  • Jizhe Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
  • Xue Li
    Department of Clinical Research Center, Dazhou Central Hospital, Dazhou 635000, China.
  • Xiaoyan Liu
    College of Information Technology, Jilin Agricultural University, Changchun, China.
  • Chunyu Wang
    School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
  • Zhixia Teng
    School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
  • Ruijie Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
  • Hongchao Lv
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
  • Maozu Guo
    School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.

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