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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 includes information on mouse genetic markers, molecular clones (probes, primers and YACs), phenotypes, sequences, comparative mapping data, graphical displays of linkage, cytogenetic and physical maps, experimental mapping data, as well as strain distribution patterns for recombinant inbred strains (RIs) and cross haplotypes.
• Sources for information in the database include the scientific literature, DNA mapping panel data produced by various researchers, the MIT Whitehead Institute (MIT genetic and physical mapping data), WashU, and the IMAGE consortium.
• MGD is closely linked with GXD's Gene Expression Literature index. This is a searchable index of references to the scientific literature reporting data on endogenous gene expression during mouse embryonic development. MGD provides links to Gene Expression Literature content records through genetic marker detail records, and in turn, the content records provide inks to MGD references and genetic marker records.
• 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 daily 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 mouse physical mapping data downloaded from MIT, data generated by the collaborative efforts of WashU, the IMAGE consortium, ATCC, and Mouse Genome Informatics. 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
• 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
• Human disease data (OMIM)
• 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, TreeFam, Uniprot, VEGA, VISTA
Sequences	GenBank, RefSeq, SWISS-PROT, TrEMBL, DFCI, DoTS, and NIA mouse gene indices
Molecular probes and clones	GenBank, EMBL, and DDBJ
References	PubMed

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 Using the Marker Summary Report and Using the Marker Detail Report 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.

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 three query forms (Genes and Markers, Phenotypes and Alleles, and Mouse Sequences). 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.

Molecular Probes and Clones

You can use the Molecular Probes and Clones Query Form to find information on probes, clones, primers, YACs, and STSs. Information may include the origin of the probe/clone, sequence, vector type, hybridizing loci, RFLPs, and references. See the Using the Molecular Probes and Clones Query Form and the Summary and Detail Help documents for more information about probe/clone records appearing in query results.

Information on genetic polymorphisms is extracted from probe/clone records in MGD. The Polymorphisms Query Form enables you to search directly for such information and display it. See Summary and Details for more information.

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Mammalian Orthology

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

Most 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. See the Evidence section under How do I interpret the results of my query? in Interpreting Mammalian Orthology Query Results for the criteria used to establish orthology.

An orthology record shows the symbol, organism, chromosome, cM position, cytogenetic band, and accession ID for each gene in the set of orthologies. Available links to other resources appear as well (e.g., Entrez Gene, HGNC, UniProt, RGD).

Every orthology assertion is supported by one or more references. The display of an orthology reference includes the J number of the reference, a short format citation, gene symbol, and organism. See What's in a Mammalian Ortholology Query Results report? for more detail.

Orthology information is presented in three other formats: Oxford Grid, comparative map and Orthology Map View. An Oxford Grid display presents an overview of orthology between two organisms. Currently, this kind of comparison is supported for the following organisms: mouse, human, cat, cattle, rat, pig, sheep, dog, chimp.

The comparative map display relies on the Linkage Map application to build a graphic display of a map of a mouse chromosome (or chromosomal region) which includes orthologies from the comparison organisms. See, for example, the comparative map for a 2 cM region around the mouse gene Chrng showing human orthology.

The Orthology Map View displays the mouse genome as the consensus genetic map, with either human or rat orthologs labeled by chromosome of origin and displayed next to the corresponding segment of the mouse genome. The Orthology Map View is accessible from the Mammalian Orthology and Comparative Maps menu.

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Sequence Data

• Vast amounts of sequence data are integrated with the biological information in MGD. Mouse sequences from GenBank, RefSeq, Swiss-Prot, DoTS, and the DFCI and NIA mouse gene indices enable powerful queries from the Mouse Sequence Query Form.
• 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.

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.

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.
  Protein Superfamily Vocabulary Browser	PIRSF superfamilies. All mapped genes for mouse, human, and rat.

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Mapping Data

MGD contains genetic mapping and linkage data, including haplotype data for linkage crosses, recombinant inbred (RI) strain distribution patterns, in situ hybridization data, deletion mapping information, translocation breakpoint mapping, somatic cell hybrids, concordance tables, congenic strains information, and physical mapping information.

Recombinant Inbred Strain Distribution Patterns Composite Data Set

The RI Data portion of MGD mapping data records has been collected and organized into composite reports accessible using the Composite Recombinant Inbred Data Sets from MGD query form. The information is displayed in tabular format with each column representing a strain and each row representing the distribution of alleles of a locus across these strains.

Recombinant Congenic Strain Distribution Patterns Composite Data Set

Composite Recombinant Congenic Strain Distribution Patterns data can be retrieved using a new query form accessed in the "Maps and Mapping Data" section of MGD. Information on four recombinant congenic strain sets is currently available. Data include the progenitor strains for each RCS set and tables showing the allelic distribution for each genetic marker that has been typed in each of the recombinant congenic strains. Each row represents the typing for a genetic marker and each column represents alleles carried by a specific recombinant congenic strain of the RCS set. Format of the report is very similar to that of the Composite Recombinant Inbred Strains distribution patterns.

For more information regarding the use of congenic strains to analyze traits controlled by multiple genes, see Peter Demant's paper,

"Recombinant Congenic Strains - A New Tool for Analyzing Genetic Traits Determined by More Than One Gene," Immunogenetics 24: 416-422, 1986.

DNA Mapping Panel Data Sets

Data from the major DNA mapping panels have been downloaded into MGD and are accessible through the DNA Mapping Panel Data Sets from MGD query form and from the Linkage Maps form. The data sets include:

Copeland-Jenkins:(C57BL/6J x M. spretus)F1 x C57BL/6J
JAX Mouse Mutant Resource BCB: (C57BL/6J x CAST/Ei)F1 x C57BL/6J
JAX Mouse Mutant Resource BSS: (C57BL/6J x SPRET/Ei)F1 x SPRET/Ei
Kozak FvC58: (NFS/N x M. spretus)F1 x C58/J Kozak FvSpr: (NFS/N x M. spretus)F1 x M. spretus
Kozak Skive: (NFS/N or C58/J x M. m. musculus)F1 x M. m. musculus
Seldin: (C3H/HeJ-Fasl<gld> x M. spretus)F1 x C3H/HeJ-Fasl<gld>
UCLA (BSB): (C57BL/6J x M. spretus)F1 x C57BL/6J

DNA Mapping Panel data may appear in tabular format, where each column represents a single offspring of the cross, and each row indicates, for each locus, which allele is present in each of the offspring. The order of rows is determined by linkage on the chromosome, and the locus nearest the centromere appears at the top of the display. Centimorgan locations for loci in the cross are determined by the provider of the cross.

Mapping Experiment Records

See Mapping Experimental Data Records for information about the content of various mapping experiment records.

Graphical Map Displays

Linkage Maps

Marker records in MGD include available information on genetic mapping locations from several sources: MGD, Chromosome Committees (up to the year 2000), and MIT. MGD provides mapping tools to generate graphic displays of genetic maps. Using the Linkage Maps form, you can generate a graphical map display in Web Map format to display linkage information for a chromosome from a particular cross. Centimorgan locations are specific to the cross and may differ from estimates for the same loci found in MGD marker records. You can print the display using the PostScript format option.

Cytogenetic Maps

MGD stores cytogenetic band information for mouse markers. The Cytogenetic Maps query form provides access to map images. Relatively few markers have been assigned cytogenetic locations.

Physical Maps

In June 1997, MGD began storing physical mapping data from MIT's mouse physical mapping project in which MIT primers and STSs are mapped against a mouse YAC library to build a contig map of the mouse. MGD provides query access to the MIT primers, STSs, and YACs. In addition, MGD provides integrated genetic/physical displays in Web Map format. These map files are updated when the MIT mapping physical mapping data set is updated.

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.

References

MGD contains references for all data in the database. By late 2007, there were over 120,000 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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