GXD: Integrated Access to Gene Expression Data from the Laboratory Mouse

Martin Ringwald
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
telephone: +1-207-288-6436
fax: +1-207-288-6132
email: ringwald@informatics.jax.org
prestype: Platform
presenter: Martin Ringwald

D.A. Begley, D.P. Hill, J.S. Beal, J.P. Corradi, G.L. Davis, J.T. Eppig, J.A. Kadin, I.J. McCright, J.E. Richardson, and M. Ringwald
The Jackson Laboratory, Bar Harbor, ME 04069, USA

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. Designed as an open-ended system that can integrate many different types of expression data, such as RNA in situ hybridization, immunohistochemistry, Northern blot, Western blot, RT-PCR, and microarray data, GXD aims to provide increasingly complete information about what transcripts and proteins are produced by what genes; where, when and in what amounts these gene products are expressed; and how their expression varies in different mouse strains and mutants. Expression patterns are described in standardized ways using an extensive dictionary of anatomical terms that has been established in collaboration with the Mouse 3D atlas project in Edinburgh, UK*, and database records are linked to digitized images of original expression data.

GXD is available at http://www.informatics.jax.org/. The database is updated and new expression data are made available on a daily basis. Data are acquired from the literature by curation staff and, increasingly, via electronic submission from laboratories. We have developed the Gene Expression Notebook, a user-friendly tool to manage expression data in the laboratory and to submit data for inclusion in GXD. GXD then places the expression data in the larger biological context, thereby providing a comprehensive framework for data storage and analysis.

GXD is integrated with the Mouse Genome Database (MGD) to enable a combined analysis of genotype, expression, and phenotype data. In collaboration with Flybase, the Saccharomyces Genome Database, and MGD we continue to build shared controlled vocabularies to describe biological processes, molecular functions and cellular components, and to assign those terms to genes and their products. These classification schemes and skilled data curation provide important new search parameters for expression data. Extensive interconnections with sequence databases and with databases from other species further extend GXD’s utility for analysis of gene expression information.

*Edinburgh collaborators: J. Bard, R. Baldock, D. Davidson, M.Kaufman
GXD is supported by NIH grant HD33745.

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