Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2004 Apr;14(4):651-60.
doi: 10.1101/gr.1974504.

Integrative Genomics: In Silico Coupling of Rat Physiology and Complex Traits With Mouse and Human Data

Affiliations
Free PMC article
Comparative Study

Integrative Genomics: In Silico Coupling of Rat Physiology and Complex Traits With Mouse and Human Data

Simon N Twigger et al. Genome Res. .
Free PMC article

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.

Figures

Figure 1
Figure 1
The Integrated Physiological Genomics Environment and VCMapView support a comparative strategy, allowing the biology mapped to organism one (e.g., QTLs, genes) to be translated to the genome and to syntenic regions in organisms 2 and 3 via the comparative maps
Figure 2
Figure 2
Display of rat Chr 14 (center) and syntenic regions in human Chr 4, 22 and 2 (left) and mouse Chr 5 and 11 (right).
Figure 3
Figure 3
Map integration of rat chromosome 16 cytogenetic, genome, and radiation hybrid provides reference information for orienting QTLs from multiple studies.
Figure 4
Figure 4
An example of integrated physiological genomics connecting 10 induced arthritis QTLs from rat Chr 10 to four arthritis QTLs in the syntenic region of mouse Chr 11. QTLs mapped in both organisms are integrated by using the respective genome and comparative maps; the maps used are labeled in the grey bar at the top of the figure.
Figure 5
Figure 5
Functional alignment of updated release of the rat radiation hybrid map RH version 3.4 aligned with the original RH version 2.1 used for quality control.
Figure 6
Figure 6
Current rat genome build (version 3.1) and earlier builds can be aligned with either genetic maps (data not shown), previous genome assemblies (version 2.1 shown), or the radiation hybrid map (RH 3.4) for overall review and quality control.

Similar articles

See all similar articles

Cited by 4 articles

Publication types

Substances

Feedback