The Mouse Genome Database genotypes::phenotypes

Abstract

The Mouse Genome Database (MGD, http://www.informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and disease. Information in MGD is obtained from diverse sources, including the scientific literature and external databases, such as EntrezGene, UniProt and GenBank. In addition to its extensive collection of phenotypic allele information for mouse genes that is curated from the published biomedical literature and researcher submission, MGI includes a comprehensive representation of mouse genes including sequence, functional (GO) and comparative information. MGD provides a data mining platform that enables the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. MGI can be accessed by a variety of methods including web-based search forms, a genome sequence browser and downloadable database reports. Programmatic access is available using web services. Recent improvements in MGD described here include the unified mouse gene catalog for NCBI Build 37 of the reference genome assembly, and improved representation of mouse mutants and phenotypes.

Figure 1.

Allele detail page for the Eng^tm1Mle targeted mutation. The ‘Phenotype summary’ section [labeled 1] displays a matrix view of phenotype terms (vertical axis) by genotypes (horizontal axis). Phenotype terms can be expanded to show more detail and each genotype abbreviation links to a page detailing the full phenotype for that genotype. The ‘Phenotypic data by genotype’ section [labeled 2] shows a table of genotypes involving Eng^tm1Mle. Each genotype can be expanded to reveal full phenotypes. All data for each of the phenotype sections of this page can be viewed using the ‘show’/‘hide’ options in the section headers.

Figure 2.

Using the new expansion features for comparing phenotypes. (A) The ‘Phenotype summary’ matrix is shown expanded for the cardiovascular system term [labeled 1]. Note the finer granularity of the terms. The genetic background effect in Eng^tm1Mle/+heterozygotes can clearly be seen. Heterozygote 4 (ht4) displays a normal cardiovascular phenotype, compared with the other two heterozygous genotypes (ht2, ht3). By glancing below to the ‘Phenotypic data by genotype’ section [labeled 2], it can be observed that in Eng^tm1Mle/+mice, the addition of background alleles from the CD-1 strain appears to confer a protective effect for these cardiovascular system phenotypes. (B) The ‘Phenotypic data by genotype’ section is shown expanded for one of the genotypes (Eng^tm1Mle/+heterozygotes in the 129P2/OlaHsd-Eng^tm1Mle strain, abbreviated ht2).

Figure 3.

Redesigned MGI Homepage. Notable design items of the new MGI web pages include a navigation bar that is included on every MGI page, featuring cascading menus that lead users quickly to the query form or information page of interest. On the homepage, clickable images representing major content areas lead users to pages with additional information, descriptions of MGD data for that area, links to query forms and reports, and relevant FAQs.

Figure 4.

New MGI search tool. The new search tool provides maximum flexibility for quickly locating genes and annotations of interest in MGI. Searches are automatically done against nomenclature (gene symbols/names, synonyms, orthologs), ontologies/vocabularies used for MGI data associations, including gene function, process and cellular location (GO), phenotype (MP) and disease terms (OMIM), anatomical terms, protein domains (PIRSF) and accession IDs. Results returned are ranked by best match to the term(s) entered by the user and links are provided to the underlying data and to a comprehensive list of matches in the database. The figure shows the results for searching for: deafness hearing NM_013627. The terms deafness and/or hearing were matched to 267 genes and 246 vocabulary terms, and the sequence ID retrieved the corresponding RefSeq match.