Exploring Genetic, Genomic, and Phenotypic Data at the Rat Genome Database
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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. 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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PDF or HTML at Wiley Online LibraryTable 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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Figure 1.14.1 The RGD home page. Tabs and links to all of the data and analysis tools at RGD are found here. The bottom half of the page covers RGD tutorial videos, new features, and a conference list for users. View Image -
Figure 1.14.2 Intermediate search results page. This page shows results grouped by category with links to the specific groups of data. View Image -
Figure 1.14.3 Gene Search page. This page provides a gene‐specific version of the RGD data search. View Image -
Figure 1.14.4 Genes results page. This page displays data across three species with multiple options for viewing and arranging the display. View Image -
Figure 1.14.5 Ontology general search page (left panel) and ontology general search results page (right panel). The page in the left panel is used to search all controlled vocabularies used at RGD. The right panel shows an intermediate results page grouping results according to ontology/vocabulary. View Image -
Figure 1.14.6 Ontology general search results details page. This page highlights the list of search result terms for a selected ontology. View Image -
Figure 1.14.7 Ontology report page. This page defines the selected ontology term, lists all RGD objects annotated with that term and its children, and displays genomic location of annotated genes, QTLs, and congenic strains. View Image -
Figure 1.14.8 Bottom of ontology report page. Underneath the annotated object list are text and graph representations of the ontology branch(s) containing the selected term. View Image -
Figure 1.14.9 The RGD ontology browser. Any of the ontologies/vocabularies used at RGD can be displayed in this horizontally oriented term browser. View Image -
Figure 1.14.10 The GViewer. All genes, QTLs, and congenic strains annotated to the selected term and its descendants are shown at the appropriate chromosomal location. View Image -
Figure 1.14.11 The QTL specific search. This page uses a keyword search with optional restrictions to narrow the search. View Image -
Figure 1.14.12 QTL search results. This page has functionality similar to the genes search results page (Fig. ). View Image -
Figure 1.14.13 Top of QTL report page including general information section and Annotation section. View Image -
Figure 1.14.14 Annotation report page. This page gives annotation information such as type of evidence, data source, number of annotations from that data source, and number of references associated with the RGD data object. View Image -
Figure 1.14.15 Genes in Region subsection of the QTL report page. View Image -
Figure 1.14.16 Position Markers subsection of the QTL report page. View Image -
Figure 1.14.17 The Additional Information section of the QTL report page. View Image -
Figure 1.14.18 A default view of rat GBrowse with an RGD genes track selected. View Image -
Figure 1.14.19 GBrowse search results page for the search term hypertension. View Image -
Figure 1.14.20 GBrowse detail page for Bp133, including view with QTL pop‐up information. View Image -
Figure 1.14.21 GBrowse track selection page. The track content of the details display is determined by the choices made on this page. View Image -
Figure 1.14.22 Phenotypes & Models home page. View Image -
Figure 1.14.23 Phenominer Database home page. View Image -
Figure 1.14.24 Rat strain selection interface. View Image -
Figure 1.14.25 Rat strain selection results page. There are options for further limiting data by clinical measurements, experimental conditions, or measurement methods. View Image -
Figure 1.14.26 Clinical Measurements selection interface. View Image -
Figure 1.14.27 Cumulated selections page. The data may be further limited by selection of Experimental Conditions and/or Measurement Methods on this page. View Image -
Figure 1.14.28 PhenoMiner report page. All the data available for the selected parameters is displayed or made accessible on this page. View Image -
Figure 1.14.29 PhenoMiner report page with extended capability displayed. View Image -
Figure 1.14.30 The top of the PhenoMiner report page showing options to “Customize chart.” View Image
Videos
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 | |
| http://rgd.mcw.edu | |
| The Rat Genome Database home page. | |
| ftp://rgd.mcw.edu/pub/ | |
| FTP site to download flat files of RGD data including genes, QTLs, microsatellites (SSLPs), maps (genetic, radiation hybrid), strains, genome annotations, and sequence files. | |
| http://mailman.mcw.edu/mailman/listinfo/rat‐forum | |
| Rat Community Forum, online bulletin board for rat‐related questions. | |
| http://www.facebook.com/pages/Rat‐Genome‐Database/108897608483 | |
| RGD on Facebook: updates on rats, rat research, and new features at the Rat Genome Database. |
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