Literature DB >> 23255149

Exploring genetic, genomic, and phenotypic data at the rat genome database.

Stanley J F Laulederkind1, G Thomas Hayman, Shur-Jen Wang, Timothy F Lowry, Rajni Nigam, Victoria Petri, Jennifer R Smith, Melinda R Dwinell, Howard J Jacob, Mary Shimoyama.   

Abstract

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.
© 2012 by John Wiley & Sons, Inc.

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Year:  2012        PMID： 23255149      PMCID： PMC3555435          DOI： 10.1002/0471250953.bi0114s40

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  9 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

3.  Using the Generic Genome Browser (GBrowse).

Authors:  Maureen J Donlin
Journal:  Curr Protoc Bioinformatics       Date:  2009-12

4.  What everybody should know about the rat genome and its online resources.

Authors:  Simon N Twigger; Kim D Pruitt; Xosé M Fernández-Suárez; Donna Karolchik; Kim C Worley; Donna R Maglott; Garth Brown; George Weinstock; Richard A Gibbs; Jim Kent; Ewan Birney; Howard J Jacob
Journal:  Nat Genet       Date:  2008-05       Impact factor: 38.330

5.  Ontology searching and browsing at the Rat Genome Database.

Authors:  Stanley J F Laulederkind; Marek Tutaj; Mary Shimoyama; G Thomas Hayman; Timothy F Lowry; Rajni Nigam; Victoria Petri; Jennifer R Smith; Shur-Jen Wang; Jeff de Pons; Melinda R Dwinell; Howard J Jacob
Journal:  Database (Oxford)       Date:  2012-03-20       Impact factor: 3.451

6.  The Rat Genome Database pathway portal.

Authors:  Victoria Petri; Mary Shimoyama; G Thomas Hayman; Jennifer R Smith; Marek Tutaj; Jeff de Pons; Melinda R Dwinell; Diane H Munzenmaier; Simon N Twigger; Howard J Jacob
Journal:  Database (Oxford)       Date:  2011-04-08       Impact factor: 3.451

7.  RGD: a comparative genomics platform.

Authors:  Mary Shimoyama; Jennifer R Smith; Tom Hayman; Stan Laulederkind; Tim Lowry; Rajni Nigam; Victoria Petri; Shur-Jen Wang; Melinda Dwinell; Howard Jacob
Journal:  Hum Genomics       Date:  2011-01       Impact factor: 4.639

8.  The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.

Authors:  Cynthia L Smith; Carroll-Ann W Goldsmith; Janan T Eppig
Journal:  Genome Biol       Date:  2004-12-15       Impact factor: 13.583

9.  The Rat Genome Database 2009: variation, ontologies and pathways.

Authors:  Melinda R Dwinell; Elizabeth A Worthey; Mary Shimoyama; Burcu Bakir-Gungor; Jeffrey DePons; Stanley Laulederkind; Timothy Lowry; Rajni Nigram; Victoria Petri; Jennifer Smith; Alexander Stoddard; Simon N Twigger; Howard J Jacob
Journal:  Nucleic Acids Res       Date:  2008-11-07       Impact factor: 16.971
  9 in total
  11 in total

1.  PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.

Authors:  Shur-Jen Wang; Stanley J F Laulederkind; G Thomas Hayman; Victoria Petri; Weisong Liu; Jennifer R Smith; Rajni Nigam; Melinda R Dwinell; Mary Shimoyama
Journal:  Database (Oxford)       Date:  2015-01-28       Impact factor: 3.451

Review 2.  2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research.

Authors:  Michael J Flister; Jeremy W Prokop; Jozef Lazar; Mary Shimoyama; Melinda Dwinell; Aron Geurts
Journal:  J Cardiovasc Transl Res       Date:  2015-04-29       Impact factor: 4.132

3.  Rat Genome Database: a unique resource for rat, human, and mouse quantitative trait locus data.

Authors:  Rajni Nigam; Stanley J F Laulederkind; G Thomas Hayman; Jennifer R Smith; Shur-Jen Wang; Timothy F Lowry; Victoria Petri; Jeff De Pons; Marek Tutaj; Weisong Liu; Pushkala Jayaraman; Diane H Munzenmaier; Elizabeth A Worthey; Melinda R Dwinell; Mary Shimoyama; Howard J Jacob
Journal:  Physiol Genomics       Date:  2013-07-23       Impact factor: 3.107

4.  Rats are the smart choice: Rationale for a renewed focus on rats in behavioral genetics.

Authors:  Clarissa C Parker; Hao Chen; Shelly B Flagel; Aron M Geurts; Jerry B Richards; Terry E Robinson; Leah C Solberg Woods; Abraham A Palmer
Journal:  Neuropharmacology       Date:  2013-06-18       Impact factor: 5.250

5.  The Rat Genome Database 2013--data, tools and users.

Authors:  Stanley J F Laulederkind; G Thomas Hayman; Shur-Jen Wang; Jennifer R Smith; Timothy F Lowry; Rajni Nigam; Victoria Petri; Jeff de Pons; Melinda R Dwinell; Mary Shimoyama; Diane H Munzenmaier; Elizabeth A Worthey; Howard J Jacob
Journal:  Brief Bioinform       Date:  2013-02-22       Impact factor: 11.622

6.  The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Authors:  Jennifer R Smith; Carissa A Park; Rajni Nigam; Stanley Jf Laulederkind; G Thomas Hayman; Shur-Jen Wang; Timothy F Lowry; Victoria Petri; Jeff De Pons; Marek Tutaj; Weisong Liu; Elizabeth A Worthey; Mary Shimoyama; Melinda R Dwinell
Journal:  J Biomed Semantics       Date:  2013-10-08

7.  The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information.

Authors:  G Thomas Hayman; Pushkala Jayaraman; Victoria Petri; Marek Tutaj; Weisong Liu; Jeff De Pons; Melinda R Dwinell; Mary Shimoyama
Journal:  Hum Genomics       Date:  2013-02-05       Impact factor: 4.639

8.  PhenoMiner: quantitative phenotype curation at the rat genome database.

Authors:  Stanley J F Laulederkind; Weisong Liu; Jennifer R Smith; G Thomas Hayman; Shur-Jen Wang; Rajni Nigam; Victoria Petri; Timothy F Lowry; Jeff de Pons; Melinda R Dwinell; Mary Shimoyama
Journal:  Database (Oxford)       Date:  2013-04-19       Impact factor: 3.451

9.  Effect of P2X4 and P2X7 receptor antagonism on the pressure diuresis relationship in rats.

Authors:  Robert I Menzies; Robert J Unwin; Ranjan K Dash; Daniel A Beard; Allen W Cowley; Brian E Carlson; John J Mullins; Matthew A Bailey
Journal:  Front Physiol       Date:  2013-10-25       Impact factor: 4.566

10.  Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.

Authors:  Rajni Nigam; Diane H Munzenmaier; Elizabeth A Worthey; Melinda R Dwinell; Mary Shimoyama; Howard J Jacob
Journal:  J Biomed Semantics       Date:  2013-11-22
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