Data Links to External Databases
Genes and Markers
Molecular Probes and Clones
MGD is updated on a weekly basis by biologists on our curatorial staff who scan the current scientific literature, extract relevant data, and enter it in MGD. Increasingly, MGD acquires data through large scale electronic transfer. Such data include sequence data from GenBank, gene models from NCBI, Ensembl, mutant alleles from ENU-mutagenesis groups and the International Knockout Mouse Consortium (IKMC). The data interface is intended to be flexible and comprehensive so that each view of particular records in MGD provides links to any related data throughout MGD and, where possible, to other databases on the Internet.
MGD contains the following kinds of information:
MGD provides links to relevant information in external databases wherever possible.
|Through...||MGD links to...|
|Markers||EC, Ensembl, Entrez, InterPro, NCBI, PDB, UniGene, Alliance of Genome Resources|
|Phenotypes||On-line Mendelian Inheritance in Man (OMIM) and the Alliance of Genome Resources for human disease data|
|SNPs and sequence polymorphisms||dbSNP|
|Homologies||Entrez, HGNC, Alliance of Genome Resources, NCBI, Ensembl Gene Tree, Uniprot|
|Sequences||GenBank, RefSeq, Uni-PROT, and TrEMBL mouse gene indices|
|Molecular probes and clones||GenBank, EMBL, DDBJ, and RIKEN|
MGD contains information on mouse genes, DNA segments, cytogenetic markers and QTLs (see Genes and Markers). Each record may include the marker symbol, name, other names or symbols and synonyms, nomenclature history, alleles, STSs, chromosomal assignment, centimorgan location, cytogenetic band, EC number (for enzymes), phenotypic classifications, human disease data, Gene Ontology (GO) terms, MGD accession IDs and supporting references. See Interpreting a Genes and Markers Summary and Interpreting Gene Details for more information about the content of the display of a marker record as it appears in the query results.
Information on alleles is stored as a separate data set (see Phenotypic Alleles). Links to alleles are provided in gene detail records. In addition, there is an Phenotypes, Alleles, and Disease Models Query Form for direct queries against the allele data set. See Details for the content of an allele record as displayed in query results.
MGD contains information on mutant alleles, transgenes, QTLs, strain characteristics, phenotype vocabularies, human disease models, and comparative phenotypes. Integrated access to phenotype and disease model data is accessible via four query forms (Genes and Markers, Phenotypes and Alleles, Human—Mouse: Disease Connection, and Batch Query). These forms provide genetic, phenotypic, and computational approaches to displaying phenotypic variation sources (single-gene, genetic mutations, QTLs, strains), as well as data on human disease correlation, and mouse models. The Human Disease Ontology (DO) Browser enables you to browse and search diseases, conditions, and syndromes directly. Phenotypic allele summary and detail reports provide detailed information about the content of phenotype records including observed phenotypes in mouse and genetic background. The Human Disease and Mouse Model Detail page lists homologous mouse and human markers where mutations in one or both species have been associated with phenotypes characteristic of this disease as well as any mouse models.
Browser Name Use this browser to search for ... GO (Gene Ontology) Browser GO term details and relationships.
Links to genes associated with your term or with any sub terms.
Mouse Developmental Anatomy Browser Anatomical structures.
Links to associated expression results.
Disease Ontology (DO) Browser Human disease terms.
Links to detail pages containing genotypes annotated with these terms.
Links to Disease Model web pages.
Mammalian Phenotype Browser Mammalian phenotype terms.
Term details and relationships among terms.
Links to genotypes annotated with each term or any sub terms.
Human Phenotype Browser Human phenotype terms.
Term details and relationships among terms.
Links to human diseases and the high-level human phenotype terms associated with the term.
Probes, clones, primers, antibodies, etc. associated with MGI data for a gene or genome feature are available via a Molecular reagents link on Gene (or genome feature) Detail pages or from a link on References -- Query Results Detail pages to Molecular Probes and Clones.
Information on genetic polymorphisms is extracted from probe/clone records in MGD.
MGD contains homology information for mouse, human, rat, and zebrafish.
MGI provides a curated set of vertebrate homologs for the research community. MGI focuses on integration of homology sets from sequenced vertebrate genomes (e.g., human, rat, zebrafish). MGI loads vertebrate orthology data based on the "stringent" set of homology class data from the Alliance of Genome Resources. The orthology inferences from different methods have been integrated using the DRSC Integrative Ortholog Prediction Tool (DIOPT). DIOPT integrates a number of existing methods including those used by the Alliance: Ensembl Compara, HGNC, Hieranoid, InParanoid, OMA, OrthoFinder, OrthoInspector, PANTHER, PhylomeDB, SonicParanoid, and ZFIN. These data include human, rat, and zebrafish homologs. In addition, we continue to work with the research community to carefully curate gene family sets, usually at the instigation of the research community.
Homologous genes associated with a mouse gene or genome feature are available from via links from the Vertebrate Homology section a Detail page for a gene/genome feature. Performing a Quick Search using a non-mouse gene or sequence accession ID returns a link to the Vertebrate Homology Class page.
MGD contains genetic mapping and linkage data, including haplotype data for linkage crosses, in situ hybridization data, deletion mapping information, translocation breakpoint mapping, somatic cell hybrids, concordance tables, congenic strains information, and physical mapping information.
Centimorgan positions for genes and markers in MGI are based on linear interpolation using the standard genetic map described in Cox et al. (2009) (PMID).
Where available, gene/genome feature detail pages provide a link to a Detailed Genetic Map that shows all markers within one cM of the marker.
In May 2005, MGD added a customized version of Lincoln Stein's Generic Genome Browser, the Mouse Genome Browser, which supports interactive browsing and display of mouse genome annotations. Access to Mouse Genome Browser is from the MGD home page (http://www.informatics.jax.org) and from the sequence map section on MGD gene detail pages. Tracks for Mouse Genome Browser include MGD representative transcripts; Ensembl and NCBI gene models; SNPs; QTLs; alleles (induced, spontaneous, gene-trapped, transgenic, targeted); phenotypes; and STS markers linked to UniSTS at NCBI. Tracks are updated at different times, depending on data availability.References Query Form, Using the References Query Form for more information about this data.
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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