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. 2004 Jan 1;32(Database issue):D476-81.
doi: 10.1093/nar/gkh125.

The Mouse Genome Database (MGD): integrating biology with the genome

Carol J Bult  1 , Judith A Blake, Joel E Richardson, James A Kadin, Janan T Eppig, R M Baldarelli, K Barsanti, M Baya, J S Beal, W J Boddy, D W Bradt, D L Burkart, N E Butler, J Campbell, R Corey, L E Corbani, S Cousins, H Dene, H J Drabkin, K Frazer, D M Garippa, L H Glass, C W Goldsmith, P L Grant, B L King, M Lennon-Pierce, J Lewis, I Lu, C M Lutz, L J Maltais, L M McKenzie, D Miers, D Modrusan, L Ni, J E Ormsby, D Qi, S Ramachandran, T B K Reddy, D J Reed, R Sinclair, D R Shaw, C L Smith, P Szauter, B Taylor, P Vanden Borre, M Walker, L Washburn, I Witham, J Winslow, Y Zhu; Mouse Genome Database Group
Affiliations

The Mouse Genome Database (MGD): integrating biology with the genome

Carol J Bult et al. Nucleic Acids Res. .

Abstract

The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

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Figures

Figure 1
Figure 1
Mouse Sequence Query Form. The new Mouse Sequence Query Form allows the user to query by sequence attributes, source attributes and properties of annotated markers including: gene symbol/name, map position, GO classification, expression (anatomical structure and Theiler stage) and phenotype. One application of the new sequence query form is positional candidate analysis, where users can request sequences annotated to genes with properties of interest within a chromosomal interval. In this example, this query form can be used to find candidates for the Idd5.1 (insulin-dependent Diabetes Mellitus 5) quantitative trait locus (QTL) that have gene products involved in the immune response and/or have defense/immunity protein activity. The query form has been set to find mRNAs for these genes that could then be used to design PCR primers for expression analysis. The query searched for RefSeq mRNAs annotated to genes within the Chr.1 interval from 6.3 to 8.6 cM with GO terms containing ‘immun’.
Figure 2
Figure 2
Sequence Summary Report. The expanded Sequence Summary Report displays the query summary at the top of the page, and provides details about the sequences returned by the query including the type, length, strain and description. In addition to links to a Sequence Detail Report, sequences can be selected and either downloaded in FASTA format or forwarded to MouseBLAST. This Summary Report shows the results from the query described in Figure 1 and shows a mRNA for each of the five genes that matched the query criteria. These genes are Cd28, Ctla4, Icos, Ccl20 and Il10.
Figure 3
Figure 3
Sequence Detail report. The new Sequence Detail report for the RefSeq record, NM_009843, shows the sequence attributes, source attributes, and the genes that have been annotated to this sequence. A summary of additional data curated for the gene is displayed with links to the detail reports for those data.
Figure 4
Figure 4
Gene Detail report. The expanded Gene Detail report now shows the coordinates for the gene on the NCBI Build 30 mouse genome sequence, and displays representative DNA (genomic), RNA and polypeptide sequences. The genomic sequence for the gene, plus a selectable amount of flanking sequence, can be downloaded in FASTA format or forwarded to MouseBLAST. Here a Gene Detail Report for the gene Ctla4 is displayed.
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References

    1. Blake J.A., Richardson.J.E., Bult,C.J., Kadin,J.A., Eppig,J.T. and the Mouse Genome Database Group (2003) MGD: the Mouse Genome Database. Nucleic Acids Res., 31, 193–195. - PMC - PubMed
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