JAX® Web News

JAX® NOTES Issue 506, Summer 2007

Two Great Databases Recently Improved

JAX® Mice Database

As part of ongoing efforts to respond to your suggestions, we have begun making significant improvements to the usability of the JAX® Mice Database. Recent users of the database may have noticed the following:

Searches for JAX® Mice strains can now be refined by specifying diseases and phenotypes.

The relationships of mouse models to human disease are stored using Online Mendelian Inheritance in Man (OMIM) terms, allowing you to browse the OMIM vocabulary for a specific genetic disorder, then directly link to a list of related strains.

The JAX® Mice Web interface now supplies links to the OMIM Database, which provides definitions of genetic diseases and contains links to other information available from the National Center for Biotechnology Information of the National Library of Medicine at the National Institutes of Health. These links enable seamless integration of information on mouse models and human disease.

Searches by phenotype use the Mammalian Phenotype Ontology developed by our Mouse Genome Informatics group. By browsing the hierarchy of the Ontology, you can "drill down" from broad to successively more specific terms and view or link to the strains related at each level of specificity. Free text notes are used to convey specific phenotypes (e.g. age of onset or severity of phenotype), which are in turn linked to references.

(Although most of the strains added to our Repository since June 2006 have been associated with phenotype terms in the database, many older strains have not. We therefore strongly encourage you to also try your search using the less specific but more comprehensively curated research area topics. We have recently been awarded an NIH grant that will support dedicated staff working to associate phenotype terms to all of the more than 3,100 JAX® Mice strains).

Mouse Phenome Database

To make the growing amount of phenotypic data in the Mouse Phenome Database (MPD) easier to use and navigate, portions of the database have been redesigned as follows:

  • Data are better categorized and can be browsed by subject area, strain, special strain set, investigator, or intervention (such as alcohol dosing or administration of high-fat diet).
  • Where possible, measurements are grouped into sets or series. For example, hearing tests at various sound frequencies are presented as a series, and cholesterol levels before and after a high-fat diet are shown as a treatment-control set. Also, strain values, overall averages, two-strain comparisons, and female-male comparisons are easier to display. It's also easier to jump to protocols.
  • With one click, you can generate graphical comparisons of dose effect, diet effect, age, and other factors.
  • To compare two strains (including SNPs between them), you can use the new two-strain comparison center.
  • Although the display and analysis tools are essentially the same as before, a new wizard helps you select measurements and use the tools.
  • If you arrive at MPD via a JAX® Mice Strain data sheet, you'll find an improved set of options to help you quickly find specific phenotype and SNP data.
  • A large new set of phenotype data has been recently released for JAX Ready Strains®, including body weight and growth curves, organ weights, blood chemistry, hematology, immunological parameters, body composition, and bone mineral density.
New Version of Gene Expression Notebook

The Gene Expression Database (GXD) recently released Gene Expression Notebook (GEN) Version 2.3.0. This version adds Excel 2004 (runs on Mac OS X). As in the previous version, this one supports Excel X for Mac and Excel 2000 and 2003 for PCs.

The GEN is an electronic tool for storing and organizing expression data and images. Implemented in Microsoft Excel, the GEN is easy to use and customize. It can store data from RNA in situ, immunohistochemistry, Northern, Western, and RT-PCR, and information on laboratory methods, reagents, and specimens. Also, the GEN can be used to easily submit mouse data to the GXD. You can download the GEN from the Mouse Genome Informatics Web site.

Gene Trap Information in MGI

Gene trapping is a high-throughput method of randomly generating mutant embryonic stem (ES) cell lines. The mutations are produced by inserting a vector construct containing a reporter gene sequence into the intron of an ES cell gene. This usually disrupts the gene's expression ("traps" it) and results in the expression of a new mRNA transcribed with the reporter gene and one or more upstream exons of the trapped gene. The new mRNA is expressed in the same cells and developmental stages as the trapped gene would have been expressed.

The International Gene Trap Consortium (IGTC) collects data on publicly available gene trap ES cell lines, and Mouse Genome Informatics (MGI) now provides links to this data from the gene's Gene Detail pages. The "Other database links" section of the MGI Gene Detail pages has a Gene Traps category listing the trapped gene's sequence tag. This tag links to NCBI, where the trapped gene's record and the provider for the ES cell line can be found. Over 10,700 mouse genes in MGI have been trapped in at least one ES cell line. Some of these lines have been used to produce mice. MGI has data on over 1,000 of the trapped genes in these lines, including curated data on the molecular definition and phenotypes of the mutant mice produced from them.

MGI will continue to curate gene trap data, and future releases of MGI will contain the sequences and genomic locations of gene trap tags.

Please send questions and comments to User Support, mgi-help@informatics.jax.org.