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 serves as a primary resource for a spectrum of genetic, genomic and biological data supporting the use of the mouse as a model for understanding human biology and disease.
• These data include the canonical mouse gene catalog, nucleotide and protein sequence associations, gene-to-function assignments based on the Gene Ontology (GO), a comprehensive catalog of mutant alleles, associations of mutant genotypes to their phenotype through the Mammalian Phenotype (MP) Ontology and to the human diseases for which they are a model through curated associations to the human Disease Ontology (DO).
• MGD provides a comprehensive genetic map, a genome browser (Mouse JBrowse) for genome viewing, a Multiple Genome Viewer (MGV) for comparing genome regions between strains and species, Single Nucleotide Polymorphisms (SNPs) and other polymorphisms and mammalian orthology data.
• Integrated with MGD are other components of the Mouse Genome Informatics (MGI) database resource. These include the Gene Expression Database (GXD), the Mouse Models of Human Cancer Database (MMHCdb), the International Mouse Strain Resource (IMSR), and the Recombinase (cre) Portal.
• Since it first became available on the web, MGD has continued to evolve, expanding its data coverage, improving data handling, and providing new data manipulation and display tools.

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, 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:

• Gene, DNA marker, QTL and Cytogenetic marker descriptions
• Mouse genetic phenotypes, genetic interrelationships, and polymorphic loci
• Human disease ontology data (DO)
• Polymorphic loci related to specified strains
• SNPs and other sequence polymorphisms
• Vertebrate homology data
• Sequence data
• Molecular probes and clones (probes, clones, primers and YACs)
• Genetic and physical mapping data
• Information on inbred strains (including M. Festing's listing)
• References supporting all data in MGD

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Data Links to External Databases

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
References	PubMed

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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 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, 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.

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Sequence Data

• Vast amounts of sequence data are integrated with the biological information in MGD. These include mouse sequences from GenBank, RefSeq, and Uni-Prot, and the Sanger Mouse Genomes Project.
• MGD contains sequence attributes such as length and provider; data about the clones the sequences were derived from; and the genes the sequences have been associated to. Because of our curated associations between mouse markers and sequences, you can search using nomenclature, map position, function (GO annotation, InterPro domain), expression (tissue and developmental stage), and phenotypes of mutant alleles.
• Source information about the clones that the sequences are derived from, such as strain, tissue, or library, is carefully translated into controlled vocabularies (see Vocabulary Browsers). This adds enormous power to sequence queries, since authors often use multiple terms to specify a strain or tissue.

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Vocabulary Browsers

• The MGD Vocabulary Browsers provide access to restricted sets of defined terms representing complex information.
• These vocabularies (known as DAGs or directed acyclic graphs) have a tree (or hierarchical) structure: terms are organized primarily by their relationship to other terms.
• The MGD Vocabulary Browsers currently available are:

  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.

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SNP Data

• MGD provides comprehensive information about reference SNPs including the reference flanking sequence, assays that comprise the SNP, gene/marker associations with their corresponding function class annotations, and links to popular gene browsers including Mouse Genome Browser and its transcript, gene model, and MGD-curated phenotype and allele tracks.
• The Mouse SNP Query Form lets you search for RefSNPs by strains, strain comparisons, RefSNP attributes, map position, marker range, or associated genes.

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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, 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.

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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 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.

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References

MGD contains references for all data in the database. By mid 2022, there were over 320,000 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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