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，用于跨多个杂交微阵列探索微阵列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（Lemkin PF等）的Java applet提供的。（2000）核酸，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，这些会话可能被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33P、Cy3/Cy5、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Cvt2Mae转换以制表符分隔的数组数据以供MAExplorer使用。NCI/CIT mAdb阵列存储系统能够以MAExplorer格式生成导出的数据-准备好进行分析。

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.