The mouse Gene Expression Database (GXD): 2007 update

Abstract

The Gene Expression Database (GXD) provides the scientific community with an extensive and easily searchable database of gene expression information about the mouse. Its primary emphasis is on developmental studies. By integrating different types of expression data, GXD aims to provide comprehensive information about expression patterns of transcripts and proteins in wild-type and mutant mice. Integration with the other Mouse Genome Informatics (MGI) databases places the gene expression information in the context of genetic, sequence, functional and phenotypic information, enabling valuable insights into the molecular biology that underlies developmental and disease processes. In recent years the utility of GXD has been greatly enhanced by a large increase in data content, obtained from the literature and provided by researchers doing large-scale in situ and cDNA screens. In addition, we have continued to refine our query and display features to make it easier for users to interrogate the data. GXD is available through the MGI web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu.shtml.

Figure 1

GXD contains detailed expression annotations. This record for an RNA in situ hybridization assay (left) illustrates the details included in annotations of expression results. It reports the reference the data were derived from, the assay type and the gene analyzed. Details regarding the nucleotide probe (or antibody) used in the assay are entered into the database and can be accessed via a link on the expression detail page; the detail page for the nucleotide probe used in this assay is pictured (upper right). In the Specimens Used section, the genetic background, age, sex and preparation method of the specimens are described; links are provided to pages that detail the characteristics of mutants used. In the Results section, we report the Theiler stage and tissue examined, as well as the level and pattern of expression as described by the author. If it is a blot assay, the number and sizes of detected bands are reported. We have permission from several publishers, as well as from researchers who have contributed data to us directly, to provide images of the original expression data (lower right) to help users analyze the results.

Figure 2

Quantity and type of detailed expression results in GXD. Since first released in June 1998, the amount of data in GXD has steadily increased to >260 000 results today. More than half of these results are from RNA in situ hybridization, immunohistochemistry and in situ reporter (knock in) assays; these studies yield complex descriptions of expression patterns. The remaining results were obtained from blot assays.

Figure 3

Querying for detailed expression data. The standard Gene Expression Data query form (left) allows users to query expression data using the parameters that are of most interest to them. Searchable fields include gene symbol/name (and synonyms); map position, anatomical structure, developmental stage and assay type. The Gene Ontology (GO) Classifications field allows users to search for genes that have specific molecular functions, are involved in particular biological processes or associated with specific subcellular components. Anatomical structures are named according to a controlled vocabulary system. Due to the hierarchical structure of this vocabulary, spatial queries can include anatomical substructures or superstructures. The Mutated Gene field allows querying for expression data in specific mutants. The query formulated in the figure uses three search parameters to ask for transcription factors expressed in the somites of N-cadherin (Cdh2) mutants. The results summary (right) lists the symbol of the gene examined, the assay type used, result details (given as an MGI accession ID linked to an assay record), allele pairs describing the mutant genotype of the specimen, age of the specimen, anatomical structure examined and whether or not expression was detected. Clicking on the boxed accession IDs will yield the detailed expression record pictured in Figure 1.