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.
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.
OS: Linux, Unix and Windows
Licence: Open Source under the Mozilla Public License 1.1 (MPL 1.1)
