GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements. The Gene Expresison Database group

Abstract

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 different types of expression data. New expression data are made available on a daily basis. Thus, GXD provides 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. GXD is integrated with the Mouse Genome Database (MGD). Continuously refined interconnections with sequence databases and with databases from other species place the gene expression information in the larger biological and analytical context. GXD is accessible through the Mouse Genome Informatics Web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu.shtm l

Figure 1

The Gene Expression Notebook. Expression results and images are entered into ‘assay sheets’ together with detailed descriptions of molecular probes, specimens and experimental conditions used. Parts of the RNA in situ hybridization assay sheet are shown at the bottom; additional worksheets for specimen and probe information are shown at the top. Information entered into the assay sheets about ‘genes’, ‘probes’, ‘probe preparation methods’, ‘specimens’ and ‘specimen preparation methods’ is automatically stored on separate worksheets (top). Alternatively, probes and specimen information, etc., can be entered directly into the respective worksheet as probes and specimens are generated in the laboratory. Identifier fields (the white fields) on the assay sheet harbor pull-down menus that list all identifiers (names) of the objects in corresponding worksheets. Upon selecting, for example, the name of a specific probe, all the other information for that probe is automatically inserted into the assay sheet. Expression patterns can be described in the form of figure legends using plain text descriptions, by entering ad-hoc terms for tissues and structures in the results record, or, preferably, by entering terms from the anatomical dictionary into the results record using cut and paste procedures. Example data shown are from GXD entry MGI:1269967; data annotated from de la Pompa et al., Development (1997), 124, 1139–1148.