The mouse Gene Expression Database (GXD): 2014 update

Abstract

The Gene Expression Database (GXD; http://www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. GXD collects different types of expression data from studies of wild-type and mutant mice, covering all developmental stages and including data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. The data are acquired from the scientific literature and from researchers, including groups doing large-scale expression studies. Integration with the other data in Mouse Genome Informatics (MGI) and interconnections with other databases places GXD's gene expression information in the larger biological and biomedical context. Since the last report, the utility of GXD has been greatly enhanced by the addition of new data and by the implementation of more powerful and versatile search and display features. Web interface enhancements include the capability to search for expression data for genes associated with specific phenotypes and/or human diseases; new, more interactive data summaries; easy downloading of data; direct searches of expression images via associated metadata; and new displays that combine image data and their associated annotations. At present, GXD includes >1.4 million expression results and 250,000 images that are accessible to our search tools.

Figure 1.

GXD assay details pages contain detailed expression annotations. This record for an RNA in situ hybridization assay illustrates the details included in GXD annotations of expression results. The Assay section reports the reference from which the data were derived, the assay type and the gene analyzed. Details regarding the nucleotide probe (or antibody) used in the assay can be accessed via the link on the page. In the ‘Results’ section, the Theiler stage and tissue examined, as well as the strength and pattern of expression as described by the author, are reported. (If this were a blot assay, the number and sizes of detected bands would also be reported.) Images of the original expression data are displayed beside the annotations describing them, allowing them to be reviewed in context. Major specimen details, such as the age and mutant alleles, are always displayed on the page. Other details, such as genetic background, sex and preparation method, can be viewed by using the ‘more’ toggle to expand that portion of the page. Assay details pages are accessed from the GXD data summaries.

Figure 2.

The Gene Expression Data Query form provides two search utilities via tabs. The Standard Search tab shown here allows users to query for expression data using one or more parameters. Searchable fields include gene symbol/name (and synonyms); anatomical structure; developmental stage/age; and assay type. The mutant/wild-type field can be used to limit searches to expression data obtained from mutants or to exclude data obtained from mutants. Integration with the other data in MGI enables searching of expression data by sets of genes that are defined by function [GO; (26)], phenotype [Mammalian Phenotype; (27)] or human disease [OMIM; (10)] terms. The Differential Expression Search tab allows biologists to search for genes that are expressed in some anatomical structures but not others and/or in some developmental stages but not others.

Figure 3.

GXD’s data summaries are detailed, interactive and incorporate images. Each search for detailed expression data returns a page with tabbed summaries for the assay results, assays, genes and images that match the search parameters. The assay results tab (upper) lists the symbol of the gene examined, provides links (indicated by arrowheads) to the result details (such as those shown in Figure 1), lists the assay type used, lists the specimen age and tissue examined (reported as an anatomical system, age and anatomical structure), indicates whether expression was detected, provides a link to accompanying images, lists allele pairs describing the mutant genotype of the specimen (if applicable) and indicates the reference the data were derived from. The up and down arrows in the column header indicate that column is sortable; one set of arrows is circled. The assay results tab (as well as the genes tab) has buttons (indicated by the arrow) that allow for the export of results in text or spreadsheet format. The images tab (lower) allows users to quickly review images of the expression data that match their search criteria. The image is displayed beside a listing of the gene(s) examined in that image, the assay type used and a link to the result details. The ‘Click to modify search’ button near the top of the summary page (shown upper) reopens the search form, allowing for further refinement.