The mouse Gene Expression Database (GXD): a community resource for developmental biologists and neuroscientists
Written by Constance M Smith   
Wednesday, 23 June 2010 10:16

The mouse Gene Expression Database (GXD): a community resource for developmental biologists and neuroscientists

Abstract: The Gene Expression Database provides the scientific community, including neuroscientists, with an extensive and easily searchable database of gene expression information about the mouse. Its primary emphasis is on developmental studies. GXD integrates data from different assay types, including RNA in situ hybridization, immunohistochemistry, in situ reporter (knock in) studies, Northern and Western blots, and RT-PCR. It includes data from wild type and mutant mice. Database entries are detailed and include the following: time and tissue of expression (or non-expression); pattern and strength of expression; numbers and sizes of detected bands (for blots); genetic background of the samples; experimental conditions used; and a description of the probe/antibody used in the assay. The majority of standardized text annotations are also accompanied by images of the original data. GXD is integrated with the Mouse Genome Database (MGD) which stores mouse genetic, genomic, and biological data, including gene information and mutant phenotype descriptions. This integration, plus links to other community databases, puts the expression data in GXD in a larger biological and analytical context. Our curators extract data from the published literature. However, researchers are encouraged to submit their expression results directly to GXD. GXD has already successfully incorporated electronically submitted data from several large-scale studies, as well as many smaller studies. Inclusion of data in GXD allows for its immediate integration with the other data in the database and makes it available for database querying, adding to its utility and increasing its exposure to the scientific community. Data submissions receive accession numbers that can be cited in publications and grant applications. The information in GXD is updated daily. It currently contains data from approximately 35,000 experiments containing over 400,000 expression results for more than 8,600 genes. There is expression data from more than 1,300 mutants. GXD is freely available through the Mouse Genome Informatics web site at http://www.informatics.jax.org. The GXD query forms and other resources can be found at http://www.informatics.jax.org/expression.shtml. GXD is funded by NICHD grant HD033745.

Constance M Smith1, Jacqueline H Finger1, Terry F Hayamizu1, Ingeborg J McCright1, Janan T Eppig1, James T Kadin1, Joel E Richardson1, Martin Ringwald1

1Mouse Genome Informatics, The Jackson Laboratory

Keywords: bioinformatics , development , embryo , gene expression

 

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