The assay page includes: publication reference, gene symbol and name, link to probe/antibody information, specimen details, and the expression annotations for each specimen

The assay page includes: publication reference, gene symbol and name, link to probe/antibody information, specimen details, and the expression annotations for each specimen. have been improved, new querying capabilities were implemented, and links to other expression resources were added. GXD is usually available through the MGI web site (www.informatics.jax.org), or directly atwww.informatics.jax.org/expression.shtml. == INTRODUCTION Mouse monoclonal to CD31 == 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 Sodium sulfadiazine large variety of database queries. GXD captures a broad spectrum of assay types, including RNAin situhybridization, 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 Sodium sulfadiazine 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). == DATA CONTENT == == Literature Summary == In the Literature Summary, GXD provides users with a way to quickly determine what mouse developmental expression data are available Sodium sulfadiazine 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,.