MGI Tutorial

For up to date issues or problems with this database please see the wiki.
For more information, please visit the Mouse Genome Informatics.

The mouse genome informatics database is a very complicated set of data, including most if not all of the known data on mouse genetics.  This makes the source very rich, but also very complicated to navigate.  NIF shows a small amount of this data at the moment and can lead into further exploration of this complicated database.  However, we do encourage the user to explore the tutorial options within the MGI site.

Mouse genome informatics database includes the following:

• 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 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
  

To find MGI data we searched for glutamate, however any gene names or receptor names should bring up many results from MGI.

The search for "Glutamate Receptor" brings up many results in the database tab and MGI can be found in the Genes category.  Note that the data that is displayed is the gene and brain region as well as associated data, including whether or not the gene is expressed (currently set to 1 or 0), organism, age of organism, assay type and name of gene.  Also, the name of the gene is often displayed many times, along side various brain region names.  The active link is in the Gene_/_Protein column, and the active link for Grik1, in this case, will take the user to the same spot within MGI.

 

Clicking on the Grik1 link above, takes the user to the following page in MGI.

This link shows data for the Chr (Chromosome number), gene symbol, name and coordinates, but to gain access to more data the user must again click on the active link to Grik1, see below.

Information about the gene, including a chromosome map,  with the current gene in red is displayed, mammalian homology, as well as phenotypes, polymorphisms, Gene Ontology, expression, molecular reagents and much more can be obtained from this page.

For more information, please visit the Mouse Genome Informatics.