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Gene Ontology, Phenotype, Pathway info
Browse the Rat Genome
Search Strains
Genes, QTL & Strains related to Disease
Data mining, analysis and visualization
Phenotypes & Traits linked to the genome
Phenotype data, Assays, Husbandry and more
Pathway reports and diagrams
Featured RGD Video Tutorials

Introduction to the Variant Visualizer

The examination of SNPs has undergone a recent change, and in response to this change, RGD has released the new Variant Visualizer tool (VarVis), taking the place of the old SNPlotyper tool. VarVis is a visualization and analysis tool for sequence variation. The data currently contains 22 rat strains sequenced by 4 independent labs.

The Gene Annotator

The Gene Annotator takes a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, and/or a chromosomal region, and retrieves annotation data from RGD. This tool will retrieve annotations from any or all ontologies used at RGD for genes and their orthologs, as well as links to additional information at other databases.

 

The Introduction to Biological Nomenclature Series

Accurate biological nomenclature is an indispensable tool used to create unambiguous annotations for genetic objects such as genes, QTLs and strains. Learn more about this valuable tool with this video series.

Click here to access RGD's Rat Community Videos page.  This page includes all of the tutorial videos that RGD has produced, plus other videos of interest to rat researchers.
 Conference Watch
Society of Toxicology 53rd Annual Meeting, Phoenix Convention Center, Phoenix, AZ, USA - March 23-27, 2014; Abstract deadline: October 7, 2013
EMBO/EMBL Symposium: Translating Diabetes, EMBL Heidelberg, Germany - March 30-April 3, 2014; Abstract Deadline: February 5, 2014
Seventh International Biocuration Conference, University of Toronto, Toronto, Canada - April 6-9, 2014; Abstract Deadline: February 10, 2014
AMIA Joint Summits on Translational Science, Parc 55 Wyndham Hotel, San Francisco, CA, USA - April 7-11, 2014; Early bird registration deadline: February 20, 2014
Experimental Biology 2014, San Diego Convention Center, San Diego, CA, USA - April 26-30, 2014; Late breaking abstract deadline: February 21, 2014
Gordon Research Conference - Cell Death Mechanisms at the Interface of Health and Disease, Mount Snow Resort, West Dover, VT, USA - June 8-13, 2014; Abstract Deadline: May 11, 2014
FASEB Research Conference - Biology of the Immune System, Snowmass, CO, USA - June 29-July 4, 2014; Abstract Deadline: May 31, 2014
DNA Habitats and its RNA Habitants, St. Virgil, Salzburg, Austria - July 3-5, 2014; Abstract Deadline: March 1, 2014
Mechanisms & Models of Cancer, Cold Spring Harbor, NY, USA - August 12-16, 2014; Abstract Deadline: May 30, 2014
Regulatory and Non-coding RNAs, Cold Spring Harbor, NY, USA - August 26-30, 2014; Abstract Deadline: June 13, 2014
Molecular Genetics of Aging, Cold Spring Harbor, NY, USA - September 29-October 3, 2014; Abstract Deadline: July 18, 2014
EMBO/EMBL Symposium: The Complex Life of mRNA, EMBL Heidelberg, Germany - October 5-8, 2014; Abstract Deadline: July 10, 2014
Biological Data Science, Cold Spring Harbor, NY, USA - November 5-8, 2014; Abstract Deadline: August 22, 2014
AMIA Annual Symposium, Washington Hilton, Washington DC, USA - November 15-19, 2014; Submission deadline: March 13, 2014
                   
Estrogen Pathway
Suite Available
The latest RGD suite provides a view of pathways that revolve around this important steroid hormone. Click here for more information.
GViewer Tool
Enhancements
The GViewer now includes additional ontologies, expanding access to newly available QTL and ChEBI data. Click here for more information.
Cisplatin & Bisphenol A
Pathways
RGD releases diagrams for the antineoplastic drug cisplatin and the pharmacotoxicology/ toxicogenomics of cisplatin and bisphenol A.
RGD Major Website
Release
RGD is pleased to announce a major website release, including updates to the data, and upgraded functionality, for a number of tools. Click here to learn more!
Acetylcholine
Signaling Pathways
RGD releases three pathways diagrams for acetylcholine signaling: an overview and signaling via the nicotinic and muscarinic receptors.
Renal Disease
Portal
RGD announces the release of the Renal Disease Portal. Click here to explore genes, QTLs and strains linked to diseases such as renal hypertension, kidney neoplasms and more, as well as associated phenotypes, pathways and biological processes.
RGD Now Links
to PhenoGen
RGD now provides links to PhenoGen Informatics, a web resource for quantitative genetics of the transcriptome. Click here to learn more!
Raw Variant Data for
28 Rat Strains
SNP and indel data in the form of vcf files for 28 rat strains recently published in the Cell paper by Atanur et al (PMID:23890820) are now available on RGD's ftp site. Click here to access the data!
Organophosphate
Response Pathway Available
RGD announces the release of the organophosphate response pathway interactive page
Variant Visualizer Accepts
Private Data
The Variant Visualizer tool has been upgraded! You can now have your data loaded and use the tool to analyze it without it becoming public. Click here to learn more.
 Latest News
    04/14 - RGD publishes the interactive diagram page for the organophosphate response pathway
    04/07 - RGD releases new pathway diagrams for acetylcholine signaling via nicotinic and muscarinic receptors along with an overview of the acetylcholine signaling system
    03/13 - RGD announces the release of the Estrogen Pathway Suite
    03/12 - RGD releases three interactive diagrams for the cisplatin drug pathway and for cisplatin and bisphenol A response pathways
    02/25 - RGD publishes a new interactive diagram for the auditory mechanotransduction pathway
    02/24 - RGD releases interactive diagrams for the retinitis pigmentosa disease pathway and associated altered visual phototransduction and altered retinoid cycle metabolic pathways
    02/02 - RGD releases comprehensive updates of the tumor necrosis factor and nuclear factor kappa B signaling pathways
    01/31 - RGD announces the addition of links to PhenoGen from rat and mouse gene pages
    01/20 - RGD publishes interactive pathway diagrams for the antihyperglycemic drug metformin as well as updated AMPK signaling and Type 2 Diabetes Mellitus pathways
    12/10 - RGD announces a major website release
    12/6 - RGD announces the release of The Balancing Blood Pressure Regulatory Mechanisms Pathway Suite Network
    11/26 - The aldosterone signaling pathway interactive diagram page now available at RGD
    11/18 - RGD releases three interactive diagram pages for the kallikrein-kinin signaling cascade and kinin signaling pathways and for angiotensin II signaling via receptor type 2
    10/29 - RGD releases a comprehensive update of the canonical Wnt signaling pathway interactive diagram page and a revised page for the altered version
    10/23 - Enhanced GViewer includes six additional searchable ontologies, expanding access to QTL and ChEBI annotation-associated genetic elements
    10/21 - RGD publishes interactive pathway diagrams for the antihypertensive drug losartan
    10/18 - Variant Visualizer upgraded to accept private data
    10/14 - The GERRC accepting gene nominations for genetically modified rats
    10/04 - RGD has updated gene, strain, QTL, disease and variant data for tracks in the rat, human and mouse genome browsers
    09/30 - RGD releases a comprehensive update of the integrin mediated signaling pathway interactive diagram page
    09/27 - Photos and artwork needed for the 2014 Rat Calendar
    09/23 - RGD releases the cerium oxide nanoparticle response pathway interactive diagram
    09/11 - RGD releases the new Renal Disease Portal
    09/05 - Updated rat Rnor5.0 Chr13 annotations now available from the Havana group
    08/19 - RGD releases the titanium dioxide nanoparticle response pathway interactive diagram page
    08/19 - RGD improves links between ontology browser and pathway diagrams
    08/05 - Variant data for 28 strains now available on RGD's ftp site
    07/17 - Sanger's HAVANA group announces rat genome annotation initiative
    06/27 - RGD releases interactive pathway diagrams for nucleotide excision repair and its altered version
    06/06 - The updated pathway suite for methionine, homocysteine, folate and related metabolites is now available at RGD
    06/03 - RGD releases the polyamine metabolic pathway interactive diagram
    05/29 - RGD's SNPlotyper tool is now available for use
    04/22 - RGD releases a suite of new interactive metabolic pathway diagrams for methionine, homocysteine, folate and related metabolites
    04/12 - Variant Visualizer tutorial video released
    04/11 - RGD releases a new tutorial on the Gene Annotator tool