The Rat Genome Database: Genetic, Genomic, and Phenotypic Data Across Multiple Species

Abstract

AbstractThe 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, https://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, cellular components, and chemical interactions 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 and other species. © 2023 Wiley Periodicals LLC.Basic Protocol 1: Navigating the Rat Genome Database (RGD) home pageBasic Protocol 2: Using the RGD search functionsBasic Protocol 3: Searching for quantitative trait lociBasic Protocol 4: Using the RGD genome browser (JBrowse) to find phenotypic annotationsBasic Protocol 5: Using OntoMate to find gene‐disease dataBasic Protocol 6: Using MOET to find gene‐ontology enrichmentBasic Protocol 7: Using OLGA to generate gene lists for analysisBasic Protocol 8: Using the GA tool to analyze ontology annotations for genesBasic Protocol 9: Using the RGD InterViewer tool to find protein interaction dataBasic Protocol 10: Using the RGD Variant Visualizer tool to find genetic variant dataBasic Protocol 11: Using the RGD Disease Portals to find disease, phenotype, and other informationBasic Protocol 12: Using the RGD Phenotypes & Models Portal to find qualitative and quantitative phenotype data and other rat strain–related informationBasic Protocol 13: Using the RGD Pathway Portal to find disease and phenotype data via molecular pathways