Faculty Collaboration Database

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database. Physiol Genomics 2016 Aug 01;48(8):589-600

Date

06/12/2016

Pubmed ID

27287925

Pubmed Central ID

PMC5005459

DOI

10.1152/physiolgenomics.00046.2016

Scopus ID

2-s2.0-84983740999 (requires institutional sign-in at Scopus site)   3 Citations

Abstract

Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality.

Author List

Wang SJ, Laulederkind SJ, Hayman GT, Petri V, Smith JR, Tutaj M, Nigam R, Dwinell MR, Shimoyama M

Authors

Melinda R. Dwinell PhD Associate Dean, Professor in the Physiology department at Medical College of Wisconsin
Stanley J. Laulederkind Research Scientist II in the Physiology department at Medical College of Wisconsin
Shur-Jen Wang Research Scientist II in the Physiology department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Animals
Cardiovascular Diseases
Databases, Genetic
Gene Ontology
Genome
Genomics
Humans
Molecular Sequence Annotation
Quantitative Trait Loci
Rats