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Published on: August 20, 2019
Analysis of disease-associated objects at the Rat Genome Database
Shur-Jen Wang1, Stanley J F Laulederkind, G T Hayman
1Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA. sjwang@mcw.edu.
Summary
The Rat Genome Database (RGD) analyzes rat genetic data, identifying shared quantitative trait loci (QTL) for cardiovascular and obesity diseases. Gene ontology analysis reveals specific biological process and cellular component enrichments linked to disease associations.
Area of Science:
- Genomics and bioinformatics
- Mammalian genetics
- Disease modeling
Background:
- The Rat Genome Database (RGD) is a key resource for laboratory rat (*Rattus norvegicus*) genetic, genomic, and phenotype data.
- RGD manually curates gene-disease associations across rat, human, and mouse models.
- Disease portals within RGD organize and present complex biological data.
Purpose of the Study:
- To analyze disease-associated rat strains, quantitative trait loci (QTL), and genes.
- To characterize enrichment patterns of gene ontology (GO) terms across different disease portals.
- To explore the relationship between GO terms and specific disease annotations.
Main Methods:
- Analysis of rat strains, QTL, and genes linked to diseases.
- Gene Ontology (GO) enrichment analysis using RatMine and DAVID functional annotation tools.
- Reciprocal examination of GO terms and disease annotations using retrieved rat gene lists.
Main Results:
- Cardiovascular disease and obesity/metabolic syndrome portals exhibit the highest concentration of rat strains and QTL, with significant overlap on chromosomes 1 and 2.
- 'Regulation of programmed cell death' and 'lipid metabolic process' were identified as key enriched biological process terms.
- Specific GO terms, when analyzed, showed clear enrichment in physiologically related diseases, enhancing disease-specific gene discovery.
Conclusions:
- The RGD resource facilitates the identification of shared genetic factors underlying complex diseases in rats.
- GO enrichment analysis provides valuable insights into the molecular mechanisms of rat diseases.
- Combining specific GO term-annotated gene sets can enhance the enrichment of neurological disease associations.
