Captures gene expression data and disseminates it to the research community.
The Gene Expression Database (GXD) captures and integrates mouse gene expression data generated by biomedical researchers worldwide. Data are acquired from the literature and via electronic data submissions from conventional laboratories and large-scale data providers, converted into standardized formats, and made freely and widely accessible to complex biological queries. A particular emphasis is on RNA in situ, immunohistochemistry, Northern blot, Western blot, RT-PCR, and cDNA source data that report on endogenous gene expression during mouse development. By combining different types of expression data and adding new data on a daily basis, GXD provides increasingly complete information about the expression profiles of transcripts and proteins in wild-type and mutant mice.
Expression patterns are recorded in a consistent and integrated manner by using the hierarchically structured Anatomical Ontology of Mouse Development built in collaboration with the Edinburgh Mouse Atlas Project (EMAP). Database records are linked to the primary image data. GXD currently holds over 260,000 images of original expression data. These images have been carefully indexed with respect to the genes analyzed, the probes used, the strain and genotype of the specimen, the developmental stages and anatomical structures in which expression was reported to be present or absent, and other parameters. One can, therefore, search for the expression data and images in many different ways.
GXD places the gene expression data in the larger biological context by interconnecting with many other data and resources. We work closely with the other Mouse Genome Informatics (MGI) projects (see also Janan T. Eppig, Ph. D., Judith A. Blake, Ph.D., and Carol J. Bult, Ph.D.) to provide the community with integrated access to genotypic, sequence, expression, functional and phenotypic data. We also supply links to many external resources such as the Allen Brain Atlas, GENSAT, EMAGE, GenePaint, Eurexpress, the European Boinformatics Institute (EBI) Expression Atlas, PubMed, Online Mendelian Inheritance in Man (OMIM), National Center for Biotechnology Information (NCBI) EntrezGene and GEO, sequence databases, InterPro and databases from other species. GXD is available through the MGI web site (http://www.informatics.jax.org/) or directly at http://www.informatics.jax.org/expression.shtml.
Anatomy ontologies are essential for the standardized description and integration of many types of biological data pertinent to anatomy, including gene expression, biological process, phenotype and pathology data. From the inception of the GXD project (see above), we have recognized this critical need and actively promoted and contributed to the development of detailed and comprehensive anatomy ontologies for both the developing and postnatal mouse. The Anatomical Ontology of Mouse Development, built, maintained, and refined in collaboration with the Edinburgh Mouse Atlas Project (EMAP), standardizes nomenclature for anatomical structures in the embryonic mouse and provides stage-specific partonomic hierarchies for relationships between developing structures. The Adult Mouse Anatomy (MA) Ontology, built, maintained, and refined by GXD, provides standardized anatomy nomenclature for the postnatal mouse, and is organized from both spatial and anatomical system perspectives (http://www.informatics.jax.org/searches/AMA_form.shtml ).
The plan is to eventually combine and integrate both ontologies into one system covering the entire lifespan of the laboratory mouse. We are also developing cross-references to anatomical ontologies from other species to support the comparative analysis of biological and biomedical data. In a previous collaboration with NCI, we have performed an in-depth comparison of the Adult Mouse Anatomical Ontology and the Human Anatomical Dictionary developed as part of the NCI Thesaurus. We extended and harmonized both anatomical ontologies and established extensive mappings between them to enable closer integration of basic science research and clinical data pertinent to cancer and other human diseases. Currently, our emphasis is on developing anatomical cross-references to other model organisms used in developmental research such as zebrafish, Xenopus and chicken.