Wrzodek Clemens, Schröder Adrian, Dräger Andreas, Wanke Dierk, Berendzen Kenneth W, Kronfeld Marcel, Harter Klaus, Zell Andreas
Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Sand 1, 72076 Tübingen, Germany.
Biosystems. 2010 Jan;99(1):79-81. doi: 10.1016/j.biosystems.2009.09.005. Epub 2009 Oct 9.
In this article we present ModuleMaster, a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the program includes all necessary data and algorithms to perform every step to find CRMs. This workbench possesses an easy-to-use graphical user interface, together with job-processing and command-line options, making ModuleMaster a sophisticated program for large-scale batch processing. The detected CRMs can be visualized and evaluated in various ways, i.e., generating GraphML- and R-based whole regulatory network visualizations or generating SBML files for subsequent analytical processing and dynamic modeling.
ModuleMaster is freely available to academics as a webstart application and for download at http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/, including comprehensive documentation.
在本文中，我们介绍了ModuleMaster，这是一种用于在共表达基因集中寻找顺式调控模块（CRM）的新型应用程序。该应用程序采用了一种新开发的方法，不仅考虑转录因子结合信息，还考虑调节因子与靶基因之间的多变量功能关系，以改进CRM的检测。仅给定微阵列和后续聚类实验的结果，该程序就包含执行寻找CRM每一步所需的所有数据和算法。这个工作台拥有易于使用的图形用户界面，以及作业处理和命令行选项，使ModuleMaster成为一个用于大规模批处理的复杂程序。检测到的CRM可以通过多种方式进行可视化和评估，例如，生成基于GraphML和R的全调控网络可视化，或生成SBML文件用于后续分析处理和动态建模。
ModuleMaster作为一个Web启动应用程序，可供学术界免费使用，并可从http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/下载，包括全面的文档。
