The mouse Gene Expression Database (GXD): 2011 update

Jacqueline H. Finger 0 Constance M. Smith 0 Terry F. Hayamizu 0 Ingeborg J. McCright 0 Janan T. Eppig 0 James A. Kadin 0 Joel E. Richardson 0 Martin Ringwald 0 0 The Jackson Laboratory , 600 Main Street, Bar Harbor, ME 04609, USA 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.informat ics.jax.org), or directly at www.informatics.jax.org/ expression.shtml. - As a primary mammalian model of human disease, the mouse is used extensively for expression studies to determine the role of genes that function in molecular pathways during developmental and disease processes. With a focus on endogenous gene expression during development, the Gene Expression Database (GXD) collects data from the scientific literature, from individual laboratories, and from large-scale data providers. It makes these data readily available to the research community in a highly curated and integrated format that allows for a large variety of database queries. GXD captures a broad spectrum of assay types, including RNA in situ hybridization, immunohistochemistry, knock-in reporter assays, northern blot, western blot, RTPCR, RNase protection and S1 nuclease assays. It covers all developmental stages and tissues and includes data from many different mouse strains and mutants, giving researchers a tool to examine the effects of mutations on gene expression. GXD forms an important and integral component of the larger Mouse Genome Informatics (MGI) resource. Therefore, the expression data are fully integrated with mouse genetic, sequence, functional and phenotypic information (14). MGI maintains further links to many other resources such as GenBank, gene model resources, Entrez Gene, UniProt, InterPro, Online Mendelian Inheritance in Man (OMIM) and the International Knockout Mouse Consortium (IKMC) among others (514). This robust integration puts the expression data in GXD into a much larger biological and analytical context. Other databases that store mouse expression information have been developed in recent years. They store data from one or two specific assay types and/or focus on specific developmental stages; they are often dedicated to specific data generation projects (1522). As will be evident from this article, GXD is working with those resources that are complementary to GXD, adding value through data integration and the implementation of new interconnections. Due to its broad scope, its extensive data curation and integration efforts, and the resulting querying capabilities, GXD continues to provide a unique resource to the biomedical research community. GXD is updated daily. GXD and its query interfaces have been described earlier (2327). Here, we report on our recent progress in terms of data acquisition, and on the implementation of new query and display features. NEW GXD HOMEPAGE To present the objectives of GXD more clearly and to make the database more intuitive to use, we redesigned the GXD homepage (www.informatics.jax.org/expression .shtml). The new layout provides clear access to the various query forms, with short descriptors for each form. The Frequently Asked Questions (FAQs) section provides links to brief on-line tutorials demonstrating how one can search for different types of data in GXD. The GXD Includes section provides information about the current data content in GXD, such as the number of genes with annotated expression data, the number of expression results and the number of images in the database. The Gene Expression News section informs users when new features, capabilities and data sets become available. A series of tabs at the bottom of the home page provides access to help documentation and data policies, information about GXD and its collaborators, and links to guidelines and tools that help researchers to submit data electronically. That GXD is also an integral component of MGI is made transparent through the use of a central Quick Search (see below), a common navigation bar and common drop-menus and tab choices that direct users to various data sets, search forms, tools and other resources. Large icons on the MGI homepage provide visual cues to the various core areas, including expression (GXD). In the Literature Summary, GXD provides users with a way to quickly determine what mouse developmental expression data are available in the scientific literature. The staff of GXD searches the scientific literature for publications that present endogenous gene expression experiments during mouse development. In a first annotation step for each publication, the genes analyzed, the ages of mice used in the experiment, and the type of experimental assay performed for each gene are recorded and entered into the database. These data are easily searched using the Gene Expression Literature Query Form. These queries can also include citation (author, journal, year) and abstract information. However, this tool takes users further than a Pubmed search because the data in the GXD Literature Summary are based on the curation of the full-text of the paper, including supplemental information, and annotations are standardized with regard to gene, age and assay type information. The Literature Summary is comprehensive and up-to-date. It includes all journal articles containing expression data during mouse development from 1993 to the present and all articles from major developmental journals since 1990. Currently, the GXD Literature Summary has 108 604 records covering data for 13 619 genes from 17 521 references. Gene expression data Beyond summaries, GXD also provides detailed records of experimental expression results. GXD assay records contain the authors description of the tissue pattern and strength of expression, translated into standard terminology (see below), the probe or antibody information available, as well as the specimen age, genetic background and preparation (Figure 1). The expression information is recorded in standardized formats by making extensive use of controlled vocabularies and ontologies, thus enabling data integration and co (...truncated)