Exploring Genetic, Genomic, and Phenotypic Data at the Rat Genome Database

Stanley J. F. Laulederkind1, G. Thomas Hayman1, Shur‐Jen Wang1, Timothy F. Lowry1, Rajni Nigam1, Victoria Petri1, Jennifer R. Smith1, Melinda R. Dwinell1, Howard J. Jacob1, Mary Shimoyama1

1 Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.14
DOI:  10.1002/0471250953.bi0114s40
Online Posting Date:  December, 2012
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The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes, and cellular components for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat. Curr. Protoc. Bioinform. 40:1.14.1‐1.14.27. © 2012 by John Wiley & Sons, Inc.

Keywords: rat; database; quantitative trait locus; ontology; genomics; gene

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Table of Contents

  • Introduction
  • Basic Protocol 1: Navigating the RGD Home Page
  • Basic Protocol 2: Using the RGD Search Functions
  • Basic Protocol 3: Searching for Quantitative Trait Loci
  • Basic Protocol 4: Using the RGD Genome Browser (GBrowse) to Find Phenotypic Annotations
  • Basic Protocol 5: Using PhenoMiner to View Quantitative Phenotype Data
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

   Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel‐Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25‐29.
   Dwinell, M.R., Worthey, E.A., Shimoyama, M., Bakir‐Gungor, B., DePons, J., Laulederkind, S., Lowry, T., Nigram, R., Petri, V., Smith, J., Stoddard, A., Twigger, S.N., Jacob, H.J.; RGD Team. 2009. The Rat Genome Database 2009: Variation, ontologies and pathways. Nucleic Acids Res. 37:D744‐D749.
   Laulederkind, S.J., Tutaj, M., Shimoyama, M., Hayman, G.T., Lowry, T.F., Nigam, R., Petri, V., Smith, J.R., Wang, S.J., de Pons, J., Dwinell, M.R., and Jacob, H.J. 2012. Ontology searching and browsing at the Rat Genome Database. Database 2012:bas016.
   Petri, V., Shimoyama, M., Hayman, G.T., Smith, J.R., Tutaj, M., de Pons, J., Dwinell, M.R., Munzenmaier, D.H., Twigger, S.N., Jacob, H.J.; RGD Team. 2011. The Rat Genome Database pathway portal. Database 2011:bar010.
   Shimoyama, M., Nigam, R., McIntosh, L.S., Nagarajan, R., Rice, T., Rao, D.C., and Dwinell, M.R. 2012. Three ontologies to define phenotype measurement data. Front. Genet. 3:87.
   Smith, C.L., Goldsmith, C.A., and Eppig, J.T. 2005. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 6:R7.
   Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12:1599‐1610.
   Twigger, S.N., Pruitt, K.D., Fernández‐Suárez, X.M., Karolchik, D., Worley, K.C., Maglott, D.R., Brown, G., Weinstock, G., Gibbs, R.A., Kent, J., Birney, E., and Jacob, H.J. 2008. What everybody should know about the rat genome and its online resources. Nat. Genet. 40:523‐527.
Key References
   Shimoyama, M., Smith, J.R., Hayman, T., Laulederkind, S., Lowry, T., Nigam, R., Petri, V., Wang, S.J., Dwinell, M., Jacob, H.; RGD Team. 2011. RGD: A comparative genomics platform. Hum. Genomics. 5:124‐129.
  Provides an overview of how to utilize all the RGD data and tools in the areas of comparative genomics.
   Dwinell et al., 2009. See above.
  The Nucleic Acids Research annual database edition provides an overview of RGD.
Internet Resources
  The Rat Genome Database home page.
  FTP site to download flat files of RGD data including genes, QTLs, microsatellites (SSLPs), maps (genetic, radiation hybrid), strains, genome annotations, and sequence files.
  Rat Community Forum, online bulletin board for rat‐related questions.
  RGD on Facebook: updates on rats, rat research, and new features at the Rat Genome Database.
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