Generic Model Organism Database Construction Set

This site is no longer maintained and frequently out of date

The current GMOD website is at www.gmod.org. If you find content here that is not replicated there, please let Scott Cain know so he can fix it.

GMOD Resources

Demos

Links to Related Projects

GMOD is supported by a specific cooperative agreement from the USDA Agricultural Research Service, and by NIH grants co-funded from the National Human Genome Research Institute and the National Institute of General Medical Sciences.

Name

GeneXplorer

Description

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.

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.

Requirements

GeneXplorer is written in Perl, and thus requires a system that is capable of running Perl.

GeneXplorer also requires the following 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.

Documentation

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

Contact

Gavin Sherlock.

Downloads

GeneXplorer is freely available under the MIT license from CPAN.

Gramene: A Comparative Mapping Resource for Grains

cain@cshl.edu