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 Mar 15;32(6):949-51.
doi: 10.1093/bioinformatics/btv690. Epub 2015 Nov 20.

LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations

Tokhir Dadaev  1 , Daniel A Leongamornlert  1 , Edward J Saunders  1 , Rosalind Eeles  2 , Zsofia Kote-Jarai  1
Affiliations

LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations

Tokhir Dadaev et al. Bioinformatics. .

Abstract

: In this article, we present LocusExplorer, a data visualization and exploration tool for genetic association data. LocusExplorer is written in R using the Shiny library, providing access to powerful R-based functions through a simple user interface. LocusExplorer allows users to simultaneously display genetic, statistical and biological data for humans in a single image and allows dynamic zooming and customization of the plot features. Publication quality plots may then be produced in a variety of file formats.

Availability and implementation: LocusExplorer is open source and runs through R and a web browser. It is available at www.oncogenetics.icr.ac.uk/LocusExplorer/ or can be installed locally and the source code accessed from https://github.com/oncogenetics/LocusExplorer

Contact: tokhir.dadaev@icr.ac.uk.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Example LocusExplorer plot for the HNF1B PrCa risk locus at Chr17q12. Two independent PrCa association signals (rs11649743 and rs4430796) had previously been reported at this region. Fine-mapping identified more strongly associated variants to describe both of these known signals (rs718961 and rs11263763, respectively), in addition to a previously unknown third independent association (rs2229295). Variants in LD with the index SNPs are colour coded and provide an indication of the boundaries of each signal. The plot also shows the density of genotyped and imputed SNPs analyzed, the distribution of Histone marks within 7 cell lines and DNase I hypersensitivity sites in 125 cell types from the ENCODE Project, positions of regulatory elements within the LNCaP cell line and genes within the region colour coded by DNA strand. The custom user track option has also been used to display an eQTL associated with downregulation of the HNF1B gene
See this image and copyright information in PMC

References

    1. Amin Al Olama A., et al. (2015) Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans. Hum. Mol. Genet., 24, 5589–5602. - PMC - PubMed
    1. Benson D.A., et al. (2004) GenBank: update. Nucleic Acids Res., 32, D23–D26. - PMC - PubMed
    1. Chang W., et al. (2015) shiny: Web Application Framework for R. R package version 0.12.1.
    1. Coetzee S.G., et al. (2012) FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic Acids Res., 40, e139. - PMC - PubMed
    1. Encode Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57–74. - PMC - PubMed