Table of Contents

About MGD
MGD Data
Data Links to External Databases
Genes and Markers
Phenotypic Alleles
Molecular Probes and Clones
Mammalian Orthology
Sequence Data
SNP Data
Vocabulary Browsers
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 human diseases in Online Mendelian Inheritance in Man database (OMIM).
• MGD provides a comprehensive genetic map, a genome browser (Mouse GBrowse) for genome viewing, 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 Tumor Biology Database (MTB), the International Mouse Strain Resource (IMSR), the Recombinase (cre) Portal and the MouseCyc database of metabolic pathways.
• 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, 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:

• Gene, DNA marker, QTL and Cytogenetic marker descriptions
• Mouse genetic phenotypes, genetic interrelationships, and polymorphic loci
• Human disease data (OMIM)
• Polymorphic loci related to specified strains
• SNPs and other sequence polymorphisms
• Mammalian orthology data
• Sequence data
• Molecular probes and clones (probes, clones, primers and YACs)
• Genetic and physical mapping data
• Information on inbred strains (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	DFCI, DoTS, EC, Ensembl, Entrez, InterPro, NCBI, PDB, UniGene, VEGA
Phenotypes	On-line Mendelian Inheritance in Man (OMIM), for human disease data.
SNPs and sequence polymorphisms	dbSNP
Orthologies	Ark-DB, BovMap, Entrez, HGNC, Homologene, NCBI, PigBase, SheepBase, Ensembl Gene Tree, Uniprot, VEGA, VISTA
Sequences	GenBank, RefSeq, SWISS-PROT, TrEMBL, DFCI, DoTS, and NIA mouse gene indices
Molecular probes and clones	GenBank, EMBL, DDBJ, IMAGE 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, formerly imbedded 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, 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 orthologous 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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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.

Mammalian Orthology

MGD contains orthology information for mouse, human, and other mammalian organisms.

Most of the information for orthologies is now downloaded from HomoloGene. Some of the information for orthologies is extracted from the published scientific literature. In general, these papers explicitly report orthology relationships and MGD reflects that published information.

Orthologous genes associated with a mouse gene or genome feature are available from via links from the Mammalian Homology section a Detail page for a gene/genome feature. Orthologs identified in MGI's curated references are available via a link from the Detail page for a reference. Performing a Quick Search using a non-mouse gene or sequence accession ID returns a link to the Orthology Summary page.

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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, Swiss-Prot, DoTS, and the DFCI and NIA mouse gene indices.
• 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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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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Vocabulary Browsers

• The MGD Vocabulary Browsers provide access to restricted sets of defined terms representing complex information.
• Some controlled vocabularies (such as the Human Disease Vocabulary Browser), have a flat structure: terms are organized alphanumerically.
• Other vocabularies (known as DAGs or directed acyclic graphs), such as the GO Browser, 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.
  The Mouse Anatomical Dictionary Browser	Anatomical structures. Links to associated expression results.
  Human Disease Vocabulary Browser	Human disease terms. Links to detail pages containing genotypes annotated with these terms. Links to Online Mendelian Inheritance in Man (OMIM) 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.

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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. Marker detail pages and Orthology results pages offer comparative maps showing all genes within 2 cM of the gene and the chromosome location for orthologous genes.

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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