Hulsen Tim, de Vlieg Jacob, Alkema Wynand
Computational Drug Discovery, CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
BMC Genomics. 2008 Oct 16;9:488. doi: 10.1186/1471-2164-9-488.
In many genomics projects, numerous lists containing biological identifiers are produced. Often it is useful to see the overlap between different lists, enabling researchers to quickly observe similarities and differences between the data sets they are analyzing. One of the most popular methods to visualize the overlap and differences between data sets is the Venn diagram: a diagram consisting of two or more circles in which each circle corresponds to a data set, and the overlap between the circles corresponds to the overlap between the data sets. Venn diagrams are especially useful when they are 'area-proportional' i.e. the sizes of the circles and the overlaps correspond to the sizes of the data sets. Currently there are no programs available that can create area-proportional Venn diagrams connected to a wide range of biological databases.
We designed a web application named BioVenn to summarize the overlap between two or three lists of identifiers, using area-proportional Venn diagrams. The user only needs to input these lists of identifiers in the textboxes and push the submit button. Parameters like colors and text size can be adjusted easily through the web interface. The position of the text can be adjusted by 'drag-and-drop' principle. The output Venn diagram can be shown as an SVG or PNG image embedded in the web application, or as a standalone SVG or PNG image. The latter option is useful for batch queries. Besides the Venn diagram, BioVenn outputs lists of identifiers for each of the resulting subsets. If an identifier is recognized as belonging to one of the supported biological databases, the output is linked to that database. Finally, BioVenn can map Affymetrix and EntrezGene identifiers to Ensembl genes.
BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used biological databases currently available. Its implementation on the World Wide Web makes it available for use on any computer with internet connection, independent of operating system and without the need to install programs locally. BioVenn is freely accessible at http://www.cmbi.ru.nl/cdd/biovenn/.
在许多基因组学项目中，会生成大量包含生物标识符的列表。查看不同列表之间的重叠情况通常很有用，这能让研究人员快速观察他们正在分析的数据集之间的异同。可视化数据集之间重叠和差异的最常用方法之一是维恩图：一种由两个或更多圆圈组成的图，其中每个圆圈对应一个数据集，圆圈之间的重叠部分对应数据集之间的重叠部分。当维恩图是“面积成比例的”时，即圆圈和重叠部分的大小与数据集的大小相对应时，维恩图特别有用。目前没有可用的程序能够创建与广泛的生物数据库相连的面积成比例的维恩图。
我们设计了一个名为BioVenn的网络应用程序，用于使用面积成比例的维恩图来总结两个或三个标识符列表之间的重叠情况。用户只需在文本框中输入这些标识符列表，然后点击提交按钮。颜色和文本大小等参数可以通过网络界面轻松调整。文本的位置可以通过“拖放”原则进行调整。输出的维恩图可以显示为嵌入在网络应用程序中的SVG或PNG图像，也可以显示为独立的SVG或PNG图像。后一种选项对于批量查询很有用。除了维恩图之外，BioVenn还会输出每个结果子集的标识符列表。如果一个标识符被识别为属于支持的生物数据库之一，输出将链接到该数据库。最后，BioVenn可以将Affymetrix和EntrezGene标识符映射到Ensembl基因。
BioVenn是一个易于使用的网络应用程序，用于从生物标识符列表生成面积成比例的维恩图。它支持来自目前可用的最常用生物数据库的广泛标识符。它在万维网上的实现使其可在任何具有互联网连接的计算机上使用，独立于操作系统，无需在本地安装程序。可通过http://www.cmbi.ru.nl/cdd/biovenn/免费访问BioVenn。
