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Mouse Genome Database Overview

Table of Contents

About MGD
MGD Data
Data Links to External Databases
Genes and Markers
Phenotypic Alleles
Vertebrate Homology
Sequence Data
Vocabulary Browsers
SNP Data
Molecular Probes and Clones
Mapping Data
References

About MGD

MGD Data

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, VEGA, 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:

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Data Links to External Databases

MGD provides links to relevant information in external databases wherever possible.

Through...MGD links to...
MarkersDFCI, DoTS, EC, Ensembl, Entrez, InterPro, NCBI, PDB, UniGene, VEGA
PhenotypesOn-line Mendelian Inheritance in Man (OMIM) for human disease data
SNPs and sequence polymorphisms   dbSNP
Homologies Entrez, HGNC, HomoloGene, NCBI, Ensembl Gene Tree, Uniprot, VEGA, VISTA
SequencesGenBank, RefSeq, SWISS-PROT, TrEMBL, DFCI, DoTS, and NIA mouse gene indices
Molecular probes and clonesGenBank, EMBL, DDBJ, IMAGE and RIKEN
ReferencesPubMed

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Genes and Markers

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, formerly embedded in phenotype descriptions, 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.

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Phenotypic Alleles

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, Batch Query and BioMart). 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 Vocabulary 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.

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Sequence Data

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Vocabulary Browsers

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SNP Data

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Molecular Probes and Clones

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.

Vertebrate Homology

MGD contains homology information for mouse, human, rat, cattle and other vertebrate organisms.

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, dog, chimp). MGI loads sequence based vertebrate homology assertions from NCBI HomoloGene. HomoloGene programmatically detects homologs among the genome features of several completely sequenced eukaryotic genomes. 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.

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Mapping Data

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).

Graphical Map Displays


Genetic Maps

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.

Physical Maps

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, NCBI, and VEGA 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. See the update notes for details.

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References

MGD contains references for all data in the database. By early 2012, there were over 175,000 entries. MGD reference format is similar to PubMed's and data for the full MGD reference are extracted from PubMed when possible. References first appear in an abbreviated format in MGD and are updated when the PubMed records become available. If PubMed does not index the journal, our curators enter the full reference into MGD manually. See the References Query Form, Using the References Query Form for more information about this data.

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Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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last database update
12/16/2014
MGI 5.20
The Jackson Laboratory