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RGD: A comparative genomics platform

DOI: 10.1186/1479-7364-5-2-124

Keywords: genomics, database, disease

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Abstract:

The Rat Genome Database (RGD) (http://rgd.mcw.edu webcite) is recognised as the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. Since 1999, RGD has provided a comprehensive catalogue of genes, quantitative trait loci (QTL) and strains, along with software tools to retrieve and display data of interest to investigators using this organism. The disease focus of these researchers often results in the use of multiple model organisms, in addition to clinical studies, in their efforts to elucidate the mechanisms and underlying genetic factors involved in human disease. To meet the needs of such users, RGD focuses its manual curation efforts on the functional, phenotype and pathway data related to specific disease areas and has integrated human and mouse data to create a comprehensive platform for comparative genomics and genetics. Several of these components are highlighted here.The wealth of data at RGD includes genes and QTLs for rat, human and mouse, as well as polymorphic markers for rat and human (Table 1). Information on inbred, outbred, mutant, congenic, consomic and other types of rat strains is also provided. A team of scientific curators validates the identity of genomic elements, provides official nomenclature and annotates these elements with functional data from published literature [1]. With more than 1.3 million published rat research papers, prioritising data for curation is a vital task, and a project approach has proved effective. Such projects revolve around gene families, molecular pathways, ultra-conserved gene sets and diseases.The disease portals (http://rgd.mcw.edu/wg/portals/ webcite) create a structure for prioritising rat data curation and integrating rat, human and mouse information, and provide a platform for researchers easily to access multiple data types related to a particular disease area (Table 2). RGD currently has portals for cardiovascular and neurological diseases, cancer, diabetes

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