Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jul 29:6:30595.
doi: 10.1038/srep30595.

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

Jin Li  1   2   3 , Limei Wang  4   5 , Tao Jiang  1 , Jizhe Wang  1 , Xue Li  1 , Xiaoyan Liu  2 , Chunyu Wang  2 , Zhixia Teng  2 , Ruijie Zhang  1 , Hongchao Lv  1 , Maozu Guo  2
Affiliations

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

Jin Li et al. Sci Rep. .

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1. ESNPO construction.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Hirschhorn J. N. & Daly M. J. Genome-wide association studies for common diseases and complex traits. Nature reviews. Genetics 6, 95–108, doi: 10.1038/nrg1521 (2005). - DOI - PubMed
    1. Haines J. L. et al.. Complement factor H variant increases the risk of age-related macular degeneration. Science 308, 419–421, doi: 10.1126/science.1110359 (2005). - DOI - PubMed
    1. Welter D. et al.. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic acids research 42, D1001–1006, doi: 10.1093/nar/gkt1229 (2014). - DOI - PMC - PubMed
    1. Beck T., Hastings R. K., Gollapudi S., Free R. C. & Brookes A. J. GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies. European journal of human genetics: EJHG 22, 949–952, doi: 10.1038/ejhg.2013.274 (2014). - DOI - PMC - PubMed
    1. Li M. J. et al.. GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic acids research 40, D1047–1054, doi: 10.1093/nar/gkr1182 (2012). - DOI - PMC - PubMed

Publication types

LinkOut - more resources