MicroArray Explorer for the data mining of expression pr

MicroArray Explorer或MAExplorer是一个开源的基于Java的数据挖掘工具，用于探索多个杂交微阵列的微阵列DNA表达数据。阵列用于监测各种生理条件下的表达谱。MAExplorer现在可以作为用户计算机上的独立应用程序使用。它最初是作为Web浏览器的Java applet（Lemkin PF，埃塔尔.等人（2000）Nucleic Acids Res. 28（22）：4452-4459。它读取用户磁盘上的数据，以创建自定义数据挖掘会话，这些会话可以设置检查点以供以后使用。它可以处理来自各种微阵列的数据，包括33 P，Cy 3/Cy 5，克隆和寡核苷酸阵列以及其他标记系统。数据转换向导程序Cvt 2 Mae转换制表符分隔的数组数据，供MAExplorer使用。NCI/CIT mAdb阵列存放系统能够生成MAExplorer格式的导出数据-随时可供分析。 数据可以在图像、散点图、直方图、表达谱图、聚类分析等中查看和直接操作。可以使用“数据过滤器”发现有趣的克隆集，该“数据过滤器”发现通过各种用户指定测试的克隆集。用户可以生成过滤的克隆报告，这些报告可以直接访问UniGene、GeneBank、NCI/CIT mAdb和其他互联网数据库。报告数据可以导出到Excel。MAExplorer帮助：1）分析单个基因的表达; 2）分析基因家族和簇的表达; 3）比较多个阵列的表达模式。 MAExplorer已经开源，可以在http://maexplorer.sourceforge.net/上免费获得。可以下载单机版 MAExplorer版本，可在Windows、Macintosh或Unix系统（Sun Solaris、Linux等）上运行。该网站还包含文档和教程。源代码可在网站上查看或修改。 添加了一个Java插件工具MAEPlugins，允许调查人员添加自己的分析方法。在这一年中，我们增加了一些Java分析插件，并扩展了 Java API，使用户更容易编写插件。 我们添加了一个R语言扩展，这样用户就可以编写“R插件”（我们称之为RLO），使用许多复杂的统计数据来扩展对MAExplorer数据的分析， 聚类和分析方法，可用于R语言。

The MicroArray Explorer or MAExplorer is an open source Java-based data mining tool for exploring microarray DNA expression data across multiple hybridized microarrays. Arrays are used to monitor expression profiles under various physiological conditions. MAExplorer is now available as a stand-alone application on a user's computer. It was initially availabe as a Java applet for Web browers ( Lemkin PF, etal. (2000) Nucleic Acids Res. 28(22): 4452-4459. It reads data on the user's disk for creating custom data mining sessions which may be checkpointed for later use. It can handle data derived from a variety of microarrays, with 33P, Cy3/Cy5, clone and oligo arrays, and other labeling systems. A data conversion wizard program Cvt2Mae converts tab-delimited array data for use by MAExplorer. The NCI/CIT mAdb array depository system is able to generate exported data in MAExplorer format - ready to analyze. Data may be viewed and directly manipulated in images, scatter plots, histograms, expression profile plots, cluster analysis, etc. Interesting sets of clones may be discovered using a "data filter" that finds a set of clones passing a variety of user-specified tests. Users may generate filtered clone reports which may directly access UniGene, GeneBank, NCI/CIT mAdb and other Internet databases. Report data may be exported to Excel. MAExplorer helps: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns for multiple arrays. MAExplorer has been made open source and is freely available on http://maexplorer.sourceforge.net/. It may be downloaded the stand-alone version of MAExplorer for running on Windows, Macintosh or Unix systems (Sun Solaris, Linux, etc). The web site also contains documentation and tutorials. The source code is available for review or modification on the Web site. A Java plugin facility, MAEPlugins, was added to allow investigators to add their own analysis methods. During this year we added a number of Java analysis plugins and extended the Java API to make it easier for users to write plugins. We added a R language extension so that users can write "R plugins" (we call these RLOs) to extend the analysis of MAExplorer data using many of the sophisticated statistics, clustering and analysis methods available for the R language.