MicroArray Explorer for Data Mining Gene Expression Patterns

The Microarray Explorer (MAExplorer) is a Java-based data-mining facility for microarray databases. It may be freely downloaded and run as a stand-alone application on your computer. The exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays.

MAExplorer is available as Open Source at http://maexplorer.sourceforge.net/ with source code. The original MAExplorer site http://www.lecb.ncifcrf.gov/MAExplorer is a mirror site without the source code and with some additional LECB specific databases. See below for details on the source distribution, executable programs, and the public license.

With MAExplorer, it is possible to: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns and outliers; 4) directly access other genomic databases for genes of interest. Previously quantified array data is copied to your local computer where it is read by MAExplorer and intermediate results as well as the data mining session state may be saved between data mining sessions.

Microarray data may be viewed and directly manipulated in array pseudoimages, scatter plots, histograms, expression profile plots, cluster analyses (similar genes, K-means or K-median, hierarchical clustering, etc.), and reports. A key feature is the gene data filters for constraining a working set of genes to those passing a variety of user-specified tests and conditions. Reports may be generated with hypertext Web access to genomic databases such as UniGene, GenBank, dbEST, LocusLink, I.M.A.G.E., NCI/CIT mAdb microarray database and other Internet databases for sets of genes found to be of interest.

A major focus of this tool is interactive data mining with access to other supporting Web genomic databases. The emphasis on direct manipulation of genes and sets of genes in graphics and tables provides a high level of interaction with the data making it easier for investigators to test ideas when looking for patterns.

The MAExplorer Open Java API is available for creating your own Java MAEPlugins. This enables you to add your own analytic tools as well as those created by other researchers to extend MAExplorer functionalty. These could include adding new analysis methods to the base system such as statistical tests, normalization, clustering, client-server, etc.

MAExplorer was initially developed by the NCI Laboratory of Experimental and Computational Biology (LECB) in collaboration with the NIDDK Laboratory of Genetics and Physiology (LGP). MAExplorer was created to help analyze microarray data for the LGP's Mammary Genome Anatomy Program (MGAP) using mouse models designed to identify and understand genetic pathways operative during normal mammary gland development and tumorigenesis. Note that data for 50 hybridized samples from the MGAP database are included as a demonstration database when you download the stand-alone version of MAExplorer.

The Reference Manual describes the details of MAExplorer as well as showing a number of screens illustrating various operations. Several tutorials are available as well.

MAExplorer is Open Source at SourceForge

You may download a) program installers for your particular computer for both MAExplorer and Cvt2Mae; b) source code for MAExplorer, MAEPlugins, and Cvt2Mae; or c) the lastest JAR files for upgrading your system without reinstalling it. Java documentation (including a design document and javadocs) for the Open Java API is also available. Currently, installable binary distributions are available at the both the SourceForge Web site as well as the LECB/NCI Web site.

The "full" Installer distributions are available on the LECB/NCI http://www.lecb.ncifcrf.gov/MAExplorer site. The latter includes both the Mammary Geneome Anatomy Program (MGAP) public microarray database as well as the full JDKs (including the Java Virtual Machines) for all operating systems.

If your computer already has a recent JDK, you will not need to download the full distribution, since you can simply copy the .jar available on the download Web page and use it to replace the existing .jar.

Mammary Genome Anatomy Program public array data

• separate files http://www.lecb.ncifcrf.gov/mae/MGAP-Array-database/
• or as a zip file at http://www.lecb.ncifcrf.gov/mae/MGAP-Array-database.zip
• or as a tar file at http://www.lecb.ncifcrf.gov/mae/MGAP-Array-database.tar

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