The laboratory mouse serves as a pivotal animal model in gene expression and function studies, because it is closely related to the human and because tissues from many different mouse strains and mutants are readily available for detailed expression analysis. Array-based methods will provide a tremendous amount of expression information. In order to take full advantage of these data, we must be able to analyse them in a broader biological context.To address these issues and to cope with the complexity of gene expression information for the mouse in general, we developed the Gene Expression Database (GXD). GXD is designed as an open-ended system that can integrate many different types of expression data, such as RNA in situ hybridisation and immunohistochemistry data, Northern and Western blot data, RT-PCR data, cDNA data and microarray 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. Through collaborative efforts with the MRC Human Genetics Unit and the University in Edinburgh, UK1, we have established a comprehensive hierarchically structured dictionary of anatomical terms for the mouse. The dictionary is used to annotate expression patterns in standardised ways and will facilitate an integrated description of expression, anatomy and phenotype/disease data. GXD is available at http://www.informatics.jax.org/. It 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 are building shared controlled vocabularies to describe biological processes, and cellular function and location of gene products. These classification schemes and the associated data curation will 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.
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