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Comprehensive Coverage of Rat Models for Human Diseases at the Rat Genome Database
Author(s) -
Wang ShurJen,
Laulederkind Stanely JF,
Smith Jennifer R,
Hayman George Thomas,
Petri Victoria,
Dwinell Melinda,
Shimoyama Mary
Publication year - 2017
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.31.1_supplement.722.14
Subject(s) - disease , biology , model organism , genome , database , quantitative trait locus , computational biology , genetics , gene , computer science , pathology , medicine
Rat Genome Database (RGD) is a model organism database where organized functional annotations for rat, mouse and human are integrated and displayed in a portal style. These annotations, either imported from other sources or manually curated at RGD are associated with genes, strains or QTL. Recently, curation efforts have been focused on diseases and 11 area‐specific disease portals have been created. In this poster RGD is presenting its curation effort on rat disease models. To facilitate searching and browsing registered rat strains are organized in a nomenclature structure (Rat Strain Ontology), where relationships with related strains are the basis of the structure. The rat strain‐disease association is made based on disease markers, genomic or genetic association curated from published literature or user submission. These curated disease annotations are organized by RGD Disease Ontology/ vocabulary to facilitate query in either very granular disease terms or a higher level broad disease branch. Three rat disease models are presented in this poster as examples to show how rats are used in human disease study and how these data are organized and displayed at RGD. We first discuss the naturally occurring rat model of Hirschsprung disease, the spotting lethal (Sl) rat. The deletion mutation of Ednrb causes aganglionic megacolon and pigmentary disorder in rats. Both the disease and coat color phenotypes were curated at RGD. Another example is the ENU‐induced malignant peripheral nerve sheath tumor (PMST) model between inbred BDIX and BDIV strains. From these two strains which exhibit different responses to ENU, several disease QTL and congenic rat strains were developed. The last example is the collection of genetically modified rats created by the “Gene Editing Rat Resource Center” by researchers at the Medical College of Wisconsin. The disease and phenotypes association of these genetic models, captured by qualitative disease and phenotype terms and the quantitative measurements of associated traits, are available at RGD. In conclusion RGD is a comprehensive data resource for the laboratory rat used in disease study . Disease and phenotype data from various sources have been integrated and organized by controlled vocabularies for easy querying and browsing by biomedical researchers. Support or Funding Information RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.