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Open Access Software

GeneXplorer: an interactive web application for microarray data visualization and analysis

Christian A Rees1, Janos Demeter2, John C Matese13, David Botstein13 and Gavin Sherlock1*

Author Affiliations

1 Dept. of Genetics, 300 Pasteur Drive, Stanford University Medical School, Stanford, CA 94305-5120, USA

2 Dept. of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA

3 Lewis-Sigler Institute for Integrative Genomics Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA

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BMC Bioinformatics 2004, 5:141  doi:10.1186/1471-2105-5-141

Published: 1 October 2004



When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data.


We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields.


The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN webcite.