Paper Info
Title
Analysis of disease-associated objects at the Rat Genome Database.
Abstract
The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. In addition to organizing biological data from rats, the RGD team focuses on manual curation of gene-disease associations for rat, human and mouse. In this work, we have analyzed disease-associated strains, quantitative trait loci (QTL) and genes from rats. These disease objects form the basis for seven disease portals. Among disease portals, the cardiovascular disease and obesity/metabolic syndrome portals have the highest number of rat strains and QTL. These two portals share 398 rat QTL, and these shared QTL are highly concentrated on rat chromosomes 1 and 2. For disease-associated genes, we performed gene ontology (GO) enrichment analysis across portals using RatMine enrichment widgets. Fifteen GO terms, five from each GO aspect, were selected to profile enrichment patterns of each portal. Of the selected biological process (BP) terms, 'regulation of programmed cell death' was the top enriched term across all disease portals except in the obesity/metabolic syndrome portal where 'lipid metabolic process' was the most enriched term. 'Cytosol' and 'nucleus' were common cellular component (CC) annotations for disease genes, but only the cancer portal genes were highly enriched with 'nucleus' annotations. Similar enrichment patterns were observed in a parallel analysis using the DAVID functional annotation tool. The relationship between the preselected 15 GO terms and disease terms was examined reciprocally by retrieving rat genes annotated with these preselected terms. The individual GO term-annotated gene list showed enrichment in physiologically related diseases. For example, the 'regulation of blood pressure' genes were enriched with cardiovascular disease annotations, and the 'lipid metabolic process' genes with obesity annotations. Furthermore, we were able to enhance enrichment of neurological diseases by combining 'G-protein coupled receptor binding' annotated genes with 'protein kinase binding' annotated genes.
Year
DOI
Venue
2013
10.1093/database/bat046
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
Keywords
Field
DocType
quantitative trait loci,genome,obesity
Genome,Rat Genome Database,Quantitative trait locus,Gene,Chromosome,Phenotype,Biology,Laboratory rat,Bioinformatics,Genetics,Protein kinase binding
Journal
Volume
ISSN
Citations 
2013
1758-0463
2
PageRank 
References 
Authors
0.44
7
12
Name
Order
Citations
PageRank
Shur-Jen Wang113813.80
Stanley J. F. Laulederkind215015.81
G. Thomas Hayman313213.77
Jennifer R. Smith413218.16
Victoria Petri513317.76
Timothy Lowry6728.88
Rajni Nigam716926.98
Melinda R Dwinell812517.82
Elizabeth A Worthey91018.65
Diane H Munzenmaier10547.06
Mary Shimoyama1120035.46
Howard J Jacob1219128.17