The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
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 GXDs 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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