Bauer Sebastian, Grossmann Steffen, Vingron Martin, Robinson Peter N
Institute of Medical Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
Bioinformatics. 2008 Jul 15;24(14):1650-1. doi: 10.1093/bioinformatics/btn250. Epub 2008 May 29.
The Ontologizer is a Java application that can be used to perform statistical analysis for overrepresentation of Gene Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer implements the standard approach to statistical analysis based on the one-sided Fisher's exact test, the novel parent-child method, as well as topology-based algorithms. A number of multiple-testing correction procedures are provided. The Ontologizer allows users to visualize data as a graph including all significantly overrepresented GO terms and to explore the data by linking GO terms to all genes/proteins annotated to the term and by linking individual terms to child terms.
The Ontologizer application is available under the terms of the GNU GPL. It can be started as a WebStart application from the project homepage, where source code is also provided: http://compbio.charite.de/ontologizer.
Ontologizer requires a Java SE 5.0 compliant Java runtime engine and GraphViz for the optional graph visualization tool.
Ontologizer是一个Java应用程序，可用于对源自实验的基因或蛋白质集合中的基因本体（GO）术语的过度代表性进行统计分析。Ontologizer实现了基于单侧Fisher精确检验、新颖的父子方法以及基于拓扑的算法的标准统计分析方法。提供了多种多重检验校正程序。Ontologizer允许用户将数据可视化为包含所有显著过度代表性GO术语的图形，并通过将GO术语链接到注释该术语的所有基因/蛋白质以及将单个术语链接到子术语来探索数据。
Ontologizer应用程序根据GNU GPL条款提供。它可以从项目主页作为WebStart应用程序启动，该主页也提供源代码：http://compbio.charite.de/ontologizer。
Ontologizer需要符合Java SE 5.0的Java运行时引擎以及用于可选图形可视化工具的GraphViz。
