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GeneXplorer is a web application that allows clustered microarray data to be browsed interactively via the web, and can be used either for research purposes, or for providing web supplements to accompany microarray publication.


GeneXplorer is still actively supported (see Contact below), but as of January 2009, we are not developing any new features for it. One thing that we may consider in the future is allowing it to use the "extended pcl" file, which allows arbitrary numbers of columns of annotation, as we are trying to do this throughout our microarray infrastructure.

Demo & Screenshots

GeneXplorer has been used to provide several web supplements for papers arising from data in the Stanford Microarray Database. As an example, see:

J Lapointe, C Li, JP Higgins, M van de Rijn, E Bair, K Montgomery, M Ferrari, L Egevad, W Rayford, U Bergerheim, et al: Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A 2004, 101:811-6.

It has been published in:

Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G. (2004). GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics 5:141


GeneXplorer is written in Perl, and thus requires a system that is capable of running Perl. GeneXplorer also requires the following Perl modules:

In addition, GeneXplorer requires the C-program, correlations, which is included in the distribution. This must be compiled with an ANSI compatible compiler, such as gcc.

The Clustered datafiles must be created using a clustering program that produces files in the cdt format. Such software includes Mike Eisen's Cluster, or XCluster.


See the README file at the download site (see below).


Gavin Sherlock.


GeneXplorer is freely available under the MIT license from CPAN.