The mouse Gene Expression Database (GXD): 2011 update

Abstract

The Gene Expression Database (GXD) is a community resource of mouse developmental expression information. GXD integrates different types of expression data at the transcript and protein level and captures expression information from many different mouse strains and mutants. GXD places these data in the larger biological context through integration with other Mouse Genome Informatics (MGI) resources and interconnections with many other databases. Web-based query forms support simple or complex searches that take advantage of all these integrated data. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. Since the last report, the GXD data content has increased significantly, the interface and data displays have been improved, new querying capabilities were implemented, and links to other expression resources were added. GXD is available through the MGI web site (www.informatics.jax.org), or directly at www.informatics.jax.org/expression.shtml.

Figure 1.

Detailed gene expression data annotations and images. An assay record for Wnt3 (left) and the accompanying image page (right). The assay page includes: publication reference, gene symbol and name, link to probe/antibody information, specimen details, and the expression annotations for each specimen. Annotations include the anatomical structures in which expression was analyzed and the strength of expression in these structures. They refer to corresponding figures in publications or electronic submissions. Whenever possible, the images are included in GXD and assay records link to those images. The image page includes: publication reference, figure label, the figure, a caption and a copyright statement of the journal or the submitter. Figures from publications often include several image panes analyzing different genes and/or genetic backgrounds. The table below the figure indicates each pane and its corresponding assay record with links to that record, as illustrated by the red circle. For images that have been spatially mapped onto the Edinburgh Mouse Atlas, the table provides a link to the corresponding entry in EMAGE.

Figure 2.

Expression data summaries. Gene detail pages in MGI feature an ‘Expression’ section that summarizes the GXD data available for the gene from a variety of perspectives: literature content, assays, results, tissues, images, developmental stages and assay types (top). Links to the respective summaries provide quick access to the actual data. Gene-specific links to the Allen Brain Atlas, GENSAT, GEO and ArrayExpress are provided as well. Assay summaries (bottom left) link to the detailed assay records (‘data’) and show camera icons to indicate assay records with image links. The image summary (bottom right) lists thumbnails of all expression images for a gene and links to the full-size image page.

Figure 3.

MGI Batch Query. Batch queries can return GXD expression data for a list of genes or sequence IDs. Affymetrix probe set IDs are also accepted as input. Because MGI maintains up-to-date mappings of microarray probe set-to-gene associations, users can easily obtain MGI information about genes for specific sets of microarray probes, such as expression, phenotypic or, as shown, human disease data. Query results are available as web page displays, as tab-delimited text files or as Excel files. The Batch Query tool can be accessed at http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=batchQF.