MicroArray Explorer: Data Mining the Expression Profiles

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作为一个独立的应用程序在用户的计算机上可以从下面列出的带有最新文档的Web站点获得，并在早期的论文（http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11071932&dopt=Abstract） Lemkin PF等中引用。（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。数据可以在图像、散点图、直方图、表达剖面图、聚类分析等中查看和直接操作。使用“数据过滤器”可以发现有趣的克隆集，该“数据过滤器”可以找到通过各种用户指定的测试的克隆集。用户可生成过滤后的克隆报告，该报告可直接访问UniGene、GeneBank、NCI/CIT mAdb等互联网数据库。报表数据可以导出为Excel。MAExplorer帮助：1)分析单个基因的表达；2)分析基因家族和基因簇的表达；3)比较多个数组的表达式模式。MAExplorer已经开源，可以在http://maexplorer.sourceforge.net/上免费获得。您可以下载MAExplorer的独立版本，以便在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。有一个Java插件工具，MAEPlugins，可以让研究人员添加他们自己的分析方法。它还允许用R语言编写插件，这样用户就可以编写“R插件”（我们称之为RLOs），使用R语言可用的许多复杂的统计、聚类和分析方法来扩展对MAExplorer数据的分析。

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 available as a stand-alone application on a user's computer from the Web site listed below with recent documentation and is referenced in an early paper (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11071932&dopt=Abstract) 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, is available to allow investigators to add their own analysis methods. It also allows plugins to be written in the R language 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.