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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H (2015) The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res 43(Database issue):D743–D750. https://doi.org/10.1093/nar/gku1026
Petri V, Jayaraman P, Tutaj M, Hayman GT, Smith JR, De Pons J, Laulederkind SJ, Lowry TF, Nigam R, Wang SJ, Shimoyama M, Dwinell MR, Munzenmaier DH, Worthey EA, Jacob HJ (2014) The pathway ontology - updates and applications. J Biomed Semantics 5(1):7. https://doi.org/10.1186/2041-1480-5-7
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi.org/10.1101/gr.1239303
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-Aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stumpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods 9(4):345–350. https://doi.org/10.1038/nmeth.1931
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H (2014) The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42(Database issue):D358–D363. https://doi.org/10.1093/nar/gkt1115
Skinner ME, Holmes IH (2010) Setting up the JBrowse genome browser. Curr Protoc Bioinformatics 32:9.13.1–9.13.13. https://doi.org/10.1002/0471250953.bi0913s32
Westesson O, Skinner M, Holmes I (2013) Visualizing next-generation sequencing data with JBrowse. Brief Bioinform 14(2):172–177. https://doi.org/10.1093/bib/bbr078
Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes IH (2016) JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol 17:66. https://doi.org/10.1186/s13059-016-0924-1
Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O’Donnell L, Oster S, Theesfeld C, Sellam A, Stark C, Breitkreutz BJ, Dolinski K, Tyers M (2017) The BioGRID interaction database: 2017 update. Nucleic Acids Res 45(D1):D369–d379. https://doi.org/10.1093/nar/gkw1102
Dwinell MR (2010) Online tools for understanding rat physiology. Brief Bioinform 11(4):431–439. https://doi.org/10.1093/bib/bbp069
Serikawa T, Mashimo T, Takizawa A, Okajima R, Maedomari N, Kumafuji K, Tagami F, Neoda Y, Otsuki M, Nakanishi S, Yamasaki K, Voigt B, Kuramoto T (2009) National BioResource Project-Rat and related activities. Exp Anim 58(4):333–341
Hermsen R, de Ligt J, Spee W, Blokzijl F, Schafer S, Adami E, Boymans S, Flink S, van Boxtel R, van der Weide RH, Aitman T, Hubner N, Simonis M, Tabakoff B, Guryev V, Cuppen E (2015) Genomic landscape of rat strain and substrain variation. BMC Genomics 16:357. https://doi.org/10.1186/s12864-015-1594-1
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29. https://doi.org/10.1038/75556
Smith CL, Goldsmith CA, Eppig JT (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6(1):R7. https://doi.org/10.1186/gb-2004-6-1-r7
Laulederkind SJ, Tutaj M, Shimoyama M, Hayman GT, Lowry TF, Nigam R, Petri V, Smith JR, Wang SJ, de Pons J, Dwinell MR, Jacob HJ (2012) Ontology searching and browsing at the Rat Genome Database. Database (Oxford) 2012:bas016. https://doi.org/10.1093/database/bas016
Acknowledgments
RGD is supported by the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health [HL64541].
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Additional information
We wish to dedicate this chapter to the memory of our colleague and longtime RGD curator Dr. Victoria Petri, who recently passed away. Her legacy lives on through the RGD Pathway Ontology and Pathway Diagrams that she created.
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Laulederkind, S.J.F. et al. (2018). A Primer for the Rat Genome Database (RGD). In: Kollmar, M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7737-6_8
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7737-6_8
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7736-9
Online ISBN: 978-1-4939-7737-6
eBook Packages: Springer Protocols