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Toxicologic Pathology, 35:456–457, 2007
C by the Society of Toxicologic Pathology
Copyright ISSN: 0192-6233 print / 1533-1601 online
DOI: 10.1080/01926230701310536
Mouse Genome Informatics (MGI) Resources for Pathology
and Toxicology
JANAN T. EPPIG, JUDITH A. BLAKE, CAROL J. BULT, JOEL E. RICHARDSON, JAMES A. KADIN, MARTIN RINGWALD,
AND THE MGI STAFF
ogy Submission interface http://tumor.informatics.jax.org/
mtbpathwi/index.do allows contributors to create records,
specify strain and genetic mutations; generate tumor diagnoses including pathology and treatment descriptions; attach
images to diagnoses; and edit and review their submitted data.
The Mouse Tumor Frequency Grid is a visualization
tool providing an overview of tumor frequencies and tumor
types in different mouse strains http://tumor.informatics.
jax.org/mtbwi/tumorFrequencyGrid.do. This interactive
Grid displays strains on the vertical axis and organs on the
horizontal axis. Color-coded cells in the Grid represent tumor
frequencies. Each colored cell is an active link, generating a
database query for the underlying data. Users can expand
the Grid axes for individual strain families and organ systems, thus “zooming-in” on specific sub-strains and tissues
of interest.
INTRODUCTION TO MGI
The Mouse Genome Informatics (MGI, http://www.
informatics.jax.org) web site supports the use of mouse as
a model system. Of particular interest to toxicologists and
pathologists are detailed descriptions of phenotypes for mice
carrying mutations on specific genetic backgrounds, the human diseases for which these mice are models, information
on the incidence and frequency of tumors in inbred and genetically engineered mice, and core data on gene characterization, gene function, and gene expression. Images of gene
expression, phenotypes, and tumors (with diagnoses) are also
provided.
There are many ways to access MGI data. First, each web
page includes a quick Search Box where a word or partial
word is entered and the type of data to be searched is specified. Second, query forms allow users to ask complex questions that involve multiple parameters and multiple types of
data. Third, MGI generates specific data files for download
and analysis. Integrated searches are enabled through use of
structured vocabularies (ontologies) for anatomy, gene function (GO), phenotypes, tumor names, and disease terms; and
by adherence to international nomenclature standards.
Data in MGI are updated continuously through semiautomated loads, curation of the primary scientific literature, and data submissions from the scientific community.
All MGI resources described below are accessible from
http://www.informatics.jax.org.
Mouse Genome Database (MGD)
http://www.informatics.jax.org
MGD, the internationally recognized community database
for mouse, integrates core data about the genetics, genomics,
and biology of the laboratory mouse. Users most frequently
begin exploring MGD through their gene of interest. A gene’s
Detail Page provides a roadmap, with summary information
and many links to deeper detail, including a genetic map,
sequence map, orthologs with other species, nucleotide and
protein sequences, phenotype summaries, SNPs, gene function (GO), gene expression (GXD links), protein domains,
molecular reagents, and references annotated to the gene.
The Phenotype Query form http://www.informatics.
jax.org/searches/allele form.shtml can be used to simultaneously search for one or more phenotype terms, e.g.,
“aortic aneurysm AND emphysema,” and users can specify
mutation types, e.g., targeted (knock-out), and genes or
genome location of interest. An additional tool for phenotype
searching is the Mammalian Phenotype Ontology browser
http://www.informatics.jax.org/searches/MP form.shtml
where phenotype terms are viewed hierarchically from general, e.g., renal/urinary system phenotype to specific, e.g.,
glomerulonephritis. Each term is directly linked to all
mutants annotated to that phenotype. Detail pages for mutant
alleles provide extensive phenotype information, data on the
Mouse Tumor Biology Database (MTB)
http://tumor.informatics.jax.org/
MTB is designed to facilitate selection of experimental
models for cancer research, evaluation of mouse genetic models of human cancer, review of patterns of mutations in specific cancers, and identification of genes commonly mutated
across a spectrum of cancers. MTB includes data on the organ and tissue of tumor origin, tumor classification, induction treatment, metastases, mouse strains, and specific genes
or mutations in the host strain or somatic changes in the
tumor.
MTB incorporates data from many laboratories that collect, image and diagnose mouse tumors. The Mouse Pathol456
Vol. 35, No. 3, 2007
MOUSE GENOME INFORMATICS (MGI)
mutation itself, disease model information, links to IMSR
(see below), and relevant images, including whole mouse
photos, histological sections, X-ray, etc.
Users also can search for human disease models in
concert with phenotype terms using the Phenotype Query
form. In addition, a Human Disease vocabulary (derived
from OMIM, Online Mendelian Inheritance in Man)
allows one to search for diseases and discover mouse
models that have been used in studies of that disease
http://www.informatics.jax.org/javawi2/servlet/WIFetch?
page=omimVocab&subset=A). Links are provided to the
OMIM human disease records and to the mouse phenotype
descriptions for the model.
Gene Expression Database (GXD)
http://www.informatics.jax.org/menus/expression menu.
shtml
GXD stores and integrates different types of expression data for mouse and makes data available in formats appropriate for comprehensive analysis. Emphasis is
on endogenous expression during development. GXD describes expression patterns using a hierarchically structured dictionary of anatomical terms. Thus, results from
assays with differing spatial resolution are standardized
and integrated; and expression patterns can be queried
at different levels of detail. Records are complemented
with images of original expression data. Data are acquired through literature curation and via electronic submission using a laboratory management tool we have developed, the Gene Expression Notebook (GEN, http://www.
informatics.jax.org/mgihome/GXD/GEN/), implemented in
Microsoft Excel.
Expression data can be searched in multiple ways. The
Gene Expression Literature Index can be used as a quick
entree into the published literature via gene, ages analyzed, and assay types used. Detailed Gene Expression
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Data can be searched using parameters such as assay
type (RNA in situ, Northern blot, RT-PCR, immunohistochemistry, etc.), genes, ages assayed, mutants, and gene
function. An expanded Gene Expression Query form allows one to specify genes expressed in some structures
or at some developmental stages, but not others. A vocabulary browser is available for exploring and searching
for data using the Mouse Anatomical Dictionary http://
www.informatics.jax.org/searches/anatdict form.shtml.
International Mouse Strain Resource (IMSR)
http://www.imsr.org
IMSR is a searchable online database of mouse strains
and stocks available worldwide, including inbred, mutant,
and genetically engineered mice. The goal of the IMSR is to
assist the international scientific community in locating and
obtaining mouse resources for research. For each strain listed
in the IMSR, users can access information about where the
strain is available from (repository holder), in what state the
strain is available (live, frozen embryo, frozen germplasm,
ES cell line), link to descriptive information about the strain,
link to data in MGD describing phenotypes of any mutations
carried by the strain, and link to a form for contacting the
strain holder to order the strain or ask for additional information. The reciprocal links between MGD phenotype records
and IMSR strain holder information allow users to approach
finding the mice they need from a gene/strain perspective or
phenotype perspective.
Janan T. Eppig, Judith A. Blake, Carol J. Bult,
Joel E. Richardson, James A. Kadin,
Martin Ringwald, and the MGI staff
The Jackson Laboratory
Bar Harbor, ME 04609, USA