The mouse genome database (MGD): new features facilitating a model system

Abstract

The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays.

Figure 1

SNP searches and displays: (A) A partial screen shot showing 18 lines (of 565) returned after searching MGI SNP data for SNPs for the gene Fgf1. (B) Details of one of the SNPs for Fgf1.

Figure 2

Protein Superfamily: MGI Pepsin superfamily page showing mouse superfamily members with associated UniProt protein links and orthologs of each gene member in human and rat. Protein sequences from this page may be downloaded in FASTA format or forwarded to the MouseBLAST tool.

Figure 3

Images of phenotypic genotypes of mice: images are being incorporated into the allele detail page for phenotypic mutants. While these currently are limited to external visible phenotypes of whole mice, in the future other relevant images such as histological or microscopic or whole animal imaging will be available. This example shows the Mreg^dsu allele record and its associated thumbnail image, with links to all images currently available for this mutation.

Figure 4

GO annotations as graphs: we provide a tabular presentation of GO information as well as a computationally generated text form of GO annotations. A new format is now available for users to visualize these data graphically. Here, a graphical view is presented for GO annotations to the Slc13a1 gene.

Figure 5

Enhanced orthology reports and comparative graphs: orthology pages now display nucleotide and protein sequences representative of the gene orthologs. These can be downloaded in FASTA format or forwarded to the MouseBLAST tool. A new mouse–human–rat comparative GO graph allows users to see similarities and differences in gene function as annotated by the respective species databases for the ortholog group being viewed. Here an example of the Apoa4 gene is shown.