Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis

9th Annual Workshop, October 28-31, 1999

Co-sponsored by the U.S. Department of Energy


RINGWALD

Gene expression database for the laboratory mouse

M. Ringwald, Jon Beal, D. Begley, G. Davis, J. T. Eppig, K. Frazer, D. Hill, J. Kadin, J. Richardson, M. Sasner, L. Trepanier

The Jackson Laboratory, Bar Harbor, Maine, USA

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. The database is designed as an open-ended system that can integrate many different types of expression data. Thus, as data accumulate, GXD can 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 is affected in different mouse strains and mutants. GXD is available at http://www.informatics.jax.org/. It is integrated with the Mouse Genome Database (MGD). Interconnections with sequence databases and with databases from other species place the gene expression information in the larger biological and analytical context.

Since the release of GXD 1.0 in June 1998, new expression data are made available on a daily basis. Data are acquired from the literature by editorial staff and via electronic submission from laboratories. We continue to work with 'large scale expression' groups that maintain their own laboratory databases from which we can download data in bulk. In addition, we have developed a flexible and customizable tool, the 'Gene Expression Notebook', that will enable conventional laboratories to manage expression data locally and to submit data to GXD. GXD currently includes RNA in situ hybridization and immunohistochemistry data, Northern and Western blot data, RT-PCR data, RNAase protection data, and mouse cDNA/EST data. Future releases will include additional types of expression data, in particular those derived from the analysis of high density cDNA arrays.

Through collaborations with the SwissProt database and the Unigene project, we are establishing new links between sequences and genes. Interconnections with the Swissport database will provide access to structural and biochemical classification schemes. Further, we began, together with MGD, Flybase, and the Saccharomyces Genome Database, to build shared controlled vocabularies to describe biological processes, and cellular function and location of gene products. These links and classification schemes, combined with skilled data curation, will provide important new search parameters for expression data.

The Gene Expression Database is supported by NIH grant HD33745.


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