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利用 Web 2.0 技术对拟南芥 GWAS 的分析和可视化。

Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.

机构信息

Center for Neurobehavioral Genetics, University of California Los Angeles, USA.

出版信息

Database (Oxford). 2011 May 23;2011:bar014. doi: 10.1093/database/bar014. Print 2011.

DOI:10.1093/database/bar014
PMID:21609965
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3243604/
Abstract

With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu/

摘要

随着大规模基因组数据成为生物学研究的常态，这些数据的存储、整合、查看和搜索已成为一个主要挑战。本文介绍了一个拟南芥数据库的开发，该数据库存储了超过 6000 个品系的地理信息和遗传多态性数据，以及 107 个表型的全基因组关联研究（GWAS）结果，这是迄今为止最大的拟南芥多态性数据和 GWAS 结果集合。利用一系列最新的 Web 2.0 技术，如 Ajax（异步 JavaScript 和 XML）、GWT（Google-Web-Toolkit）、MVC（模型-视图-控制器）Web 框架和对象关系映射，我们为数据库创建了一个基于 Web 的应用程序（Web 应用程序），提供了地理信息、遗传多态性和 GWAS 结果的集成和动态视图。该 Web 应用程序中集成了基本的搜索功能，以辅助反向遗传学研究。该数据库及其 Web 应用程序已被证明是拟南芥社区的宝贵资源。整个框架为如何通过 Web 呈现和访问生物数据（特别是 GWAS）提供了一个示例。最后，我们通过两个示例说明了通过 Web 应用程序获得新见解的潜力，展示了如何使用它来促进正向和反向遗传学研究。数据库网址：http://arabidopsis.usc.edu/

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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a2ac/3243604/23c58861571a/bar014f12.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a2ac/3243604/c64bc8633ea3/bar014f13.jpg
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