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. 2002 Jan 1;30(1):125-8.
doi: 10.1093/nar/30.1.125.

Rat Genome Database (RGD): mapping disease onto the genome

Simon Twigger  1 , Jian Lu, Mary Shimoyama, Dan Chen, Dean Pasko, Hanping Long, Jessica Ginster, Chin-Fu Chen, Rajni Nigam, Anne Kwitek, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Howard Jacob, Peter J Tonellato
Affiliations

Rat Genome Database (RGD): mapping disease onto the genome

Simon Twigger et al. Nucleic Acids Res. .

Abstract

The Rat Genome Database (RGD, http://rgd.mcw.edu) is an NIH-funded project whose stated mission is 'to collect, consolidate and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community'. In a collaboration between the Bioinformatics Research Center at the Medical College of Wisconsin, the Jackson Laboratory and the National Center for Biotechnology Information, RGD has been created to meet these stated aims. The rat is uniquely suited to its role as a model of human disease and the primary focus of RGD is to aid researchers in their study of the rat and in applying their results to studies in a wider context. In support of this we have integrated a large amount of rat genetic and genomic resources in RGD and these are constantly being expanded through ongoing literature and bulk dataset curation. RGD version 2.0, released in June 2001, includes curated data on rat genes, quantitative trait loci (QTL), microsatellite markers and rat strains used in genetic and genomic research. VCMap, a dynamic sequence-based homology tool was introduced, and allows researchers of rat, mouse and human to view mapped genes and sequences and their locations in the other two organisms, an essential tool for comparative genomics. In addition, RGD provides tools for gene prediction, radiation hybrid mapping, polymorphic marker selection and more. Future developments will include the introduction of disease-based curation expanding the curated information to cover popular disease systems studied in the rat. This will be integrated with the emerging rat genomic sequence and annotation pipelines to provide a high-quality disease-centric resource, applicable to human and mouse via comparative tools such as VCMap. RGD has a defined community outreach focus with a Visiting Scientist program and the Rat Community Forum, a web-based forum for rat researchers and others interested in using the rat as an experimental model. Thus, RGD is not only a valuable resource for those working with the rat but also for researchers in other model organisms wishing to harness the existing genetic and physiological data available in the rat to complement their own work.

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Figures

Figure 1
Figure 1
Comparative maps of rat, human and mouse.
See this image and copyright information in PMC

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References

    1. Rapp J.P. (2000) Genetic analysis of inherited hypertension in the rat. Physiol. Rev., 80, 135–172. - PubMed
    1. Shepel L.A., Lan,H., Haag,J.D., Brasic,G.M., Gheen,M.E., Simon,J.S., Hoff,P., Newton,M.A. and Gould,M.N. (1998) Genetic identification of multiple loci that control breast cancer susceptibility in the rat. Genetics, 149, 289–299. - PMC - PubMed
    1. Remmers E.F., Longman,R.E., Du,Y., O‘Hare,A., Cannon,G.W., Griffiths,M.M. and Wilder,R.L. (1996) A genome scan localizes five non-MHC loci controlling collagen-induced arthritis in rats. Nature Genet., 14, 82–85. - PubMed
    1. Jacob H.J., Pettersson,A., Wilson,D., Mao,Y., Lernmark,A. and Lander,E.S. (1992) Genetic dissection of autoimmune type I diabetes in the BB rat. Nature Genet., 2, 56–60. - PubMed
    1. Blake J.A., Eppig,J.T., Richardson,J.E., Bult,C.J. and Kadin,J.A. (2001) The Mouse Genome Database (MGD): integration nexus for the laboratory mouse. Nucleic Acids Res., 29, 91–94. Updated article in this issue: Nucleic Acids Res. (2002), 30, 113–115. - PMC - PubMed

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