GeneExp, 310 South Third Street, San Jose, CA 95112, USA.
BMC Bioinformatics. 2010 Aug 20;11:433. doi: 10.1186/1471-2105-11-433.
In the last decade, a large amount of microarray gene expression data has been accumulated in public repositories. Integrating and analyzing high-throughput gene expression data have become key activities for exploring gene functions, gene networks and biological pathways. Effectively utilizing these invaluable microarray data remains challenging due to a lack of powerful tools to integrate large-scale gene-expression information across diverse experiments and to search and visualize a large number of gene-expression data points.
Gene Expression Browser is a microarray data integration, management and processing system with web-based search and visualization functions. An innovative method has been developed to define a treatment over a control for every microarray experiment to standardize and make microarray data from different experiments homogeneous. In the browser, data are pre-processed offline and the resulting data points are visualized online with a 2-layer dynamic web display. Users can view all treatments over control that affect the expression of a selected gene via Gene View, and view all genes that change in a selected treatment over control via treatment over control View. Users can also check the changes of expression profiles of a set of either the treatments over control or genes via Slide View. In addition, the relationships between genes and treatments over control are computed according to gene expression ratio and are shown as co-responsive genes and co-regulation treatments over control.
Gene Expression Browser is composed of a set of software tools, including a data extraction tool, a microarray data-management system, a data-annotation tool, a microarray data-processing pipeline, and a data search & visualization tool. The browser is deployed as a free public web service (http://www.ExpressionBrowser.com) that integrates 301 ATH1 gene microarray experiments from public data repositories (viz. the Gene Expression Omnibus repository at the National Center for Biotechnology Information and Nottingham Arabidopsis Stock Center). The set of Gene Expression Browser software tools can be easily applied to the large-scale expression data generated by other platforms and in other species.
在过去的十年中，大量的基因表达数据已经在公共数据库中积累。整合和分析高通量基因表达数据已成为探索基因功能、基因网络和生物途径的关键活动。由于缺乏强大的工具来整合不同实验中的大规模基因表达信息，以及搜索和可视化大量基因表达数据点，有效地利用这些宝贵的微阵列数据仍然具有挑战性。
基因表达浏览器是一个具有基于网络的搜索和可视化功能的微阵列数据集成、管理和处理系统。已经开发出一种创新的方法来定义每个微阵列实验的处理与对照，以标准化和使来自不同实验的微阵列数据一致。在浏览器中，数据在线下进行预处理，然后在线可视化生成的数据点，使用两层动态网络显示。用户可以通过基因视图查看影响选定基因表达的所有处理与对照，通过处理与对照视图查看选定处理与对照中变化的所有基因。用户还可以通过幻灯片视图检查一组处理与对照或基因的表达谱变化。此外，根据基因表达比率计算基因与处理与对照之间的关系，并显示为共响应基因和共调节处理与对照。
基因表达浏览器由一组软件工具组成，包括数据提取工具、微阵列数据管理系统、数据注释工具、微阵列数据处理管道和数据搜索和可视化工具。该浏览器作为一个免费的公共网络服务（http://www.ExpressionBrowser.com）部署，集成了来自公共数据库（即国家生物技术信息中心的基因表达综合数据库和诺丁汉拟南芥库存中心）的 301 个 ATH1 基因微阵列实验。这组基因表达浏览器软件工具可以很容易地应用于其他平台和其他物种产生的大规模表达数据。
