LocusTrack: Integrated visualization of GWAS results and genomic annotation.

Q2 Decision Sciences Source Code for Biology and Medicine Pub Date : 2015-02-03 eCollection Date: 2015-01-01 DOI:10.1186/s13029-015-0032-8

Gabriel Cuellar-Partida, Miguel E Renteria, Stuart MacGregor

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引用次数: 31

Abstract

Background: Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechanisms underlying GWAS-identified loci.

Results: We developed LocusTrack, a web-based application that annotates and creates plots of regional GWAS results and incorporates user-specified tracks that display annotations such as linkage disequilibrium (LD), phylogenetic conservation, chromatin state, and other genomic and regulatory elements. Currently, LocusTrack can integrate annotation tracks from the UCSC genome-browser as well as from any tracks provided by the user.

Conclusion: LocusTrack is an easy-to-use application and can be accessed at the following URL: http://gump.qimr.edu.au/general/gabrieC/LocusTrack/. Users can upload and manage GWAS results and select from and/or provide annotation tracks using simple and intuitive menus. LocusTrack scripts and associated data can be downloaded from the website and run locally.

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locstrack: GWAS结果和基因组注释的集成可视化。

背景:全基因组关联研究(GWAS)是复杂性状和疾病定位的重要工具。基因组注释的目视检查可用于深入了解gwas鉴定位点的生物学机制。结果:我们开发了基于web的locstrack应用程序，该应用程序注释和创建区域GWAS结果图，并包含用户指定的轨迹，显示诸如连锁不平衡(LD)，系统发育保守，染色质状态以及其他基因组和调控元件的注释。目前，locstrack可以集成来自UCSC基因组浏览器的注释轨道以及来自用户提供的任何轨道。结论:locstrack是一个易于使用的应用程序，可以通过以下URL访问:http://gump.qimr.edu.au/general/gabrieC/LocusTrack/。用户可以上传和管理GWAS结果，并使用简单直观的菜单选择和/或提供注释轨道。可以从网站下载LocusTrack脚本和相关数据并在本地运行。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Source Code for Biology and Medicine Decision Sciences-Information Systems and Management

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期刊介绍： Source Code for Biology and Medicine is a peer-reviewed open access, online journal that publishes articles on source code employed over a wide range of applications in biology and medicine. The journal"s aim is to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.

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