Faculty Collaboration Database

Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. Genome Res 2004 Apr;14(4):651-60 PMID: 15060006 PMCID: PMC383309

Pubmed ID

15060006

Abstract

Integration of the large variety of genome maps from several organisms provides the mechanism by which physiological knowledge obtained in model systems such as the rat can be projected onto the human genome to further the research on human disease. The release of the rat genome sequence provides new information for studies using the rat model and is a key reference against which existing and new rat physiological results can be aligned. Previously, we described comparative maps of the rat, mouse, and human based on EST sequence comparisons combined with radiation hybrid maps. Here, we use new data and introduce the Integrated Genomics Environment, an extensive database of curated and integrated maps, markers, and physiological results. These results are integrated by using VCMapview, a java-based map integration and visualization tool. This unique environment allows researchers to relate results from cytogenetic, genetic, and radiation hybrid studies to the genome sequence and compare regions of interest between human, mouse, and rat. Integrating rat physiology with mouse genetics and clinical results from human by using the respective genomes provides a novel route to capitalize on comparative genomics and the strengths of model organism biology.

Author List

Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ

Author

Mary E. Shimoyama PhD Associate Professor in the Biomedical Engineering department at Medical College of Wisconsin

Scopus

2-s2.0-3042536890   17 Citations

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

Animals
Chromosome Mapping
Computational Biology
Databases, Genetic
Expressed Sequence Tags
Gene Order
Genetic Markers
Genome
Genome, Human
Genomics
Humans
Mice
Multifactorial Inheritance
Quantitative Trait Loci
Quantitative Trait, Heritable
Radiation Hybrid Mapping
Rats
Software