Nature Genetics 38, 234 - 239 (2006)
Published online: 15 January 2006; | doi:10.1038/ng1693
Physiogenomic resources for rat models of heart, lung and blood disordersRenae L Malek1, Hong-ying Wang1, Anne E Kwitek2, Andrew S Greene2, Nirmal Bhagabati1, Gretta Borchardt2, Lisa Cahill1, Tracey Currier1, Bryan Frank1, Xianping Fu2, Michael Hasinoff2, Eleanor Howe1, Noah Letwin1, Truong V Luu1, Alexander Saeed1, Hedieh Sajadi1, Steven L Salzberg1, Razvan Sultana1, Mathangi Thiagarajan1, Jennifer Tsai1, Kathleen Veratti1, Joseph White1, John Quackenbush1, Howard J Jacob2
& Norman H Lee11
TREX, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA. 2
PhysGen, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA.
Correspondence should be addressed to Norman H Lee nhlee@tigr.org Cardiovascular disorders are influenced by genetic and environmental factors. The TIGR rodent expression web-based resource (TREX) contains over 2,200 microarray hybridizations, involving over 800 animals from 18 different rat strains. These strains comprise genetically diverse parental animals and a panel of chromosomal substitution strains derived by introgressing individual chromosomes from normotensive Brown Norway (BN/NHsdMcwi) rats into the background of Dahl salt sensitive (SS/JrHsdMcwi) rats. The profiles document gene-expression changes in both genders, four tissues (heart, lung, liver, kidney) and two environmental conditions (normoxia, hypoxia). This translates into almost 400 high-quality direct comparisons (not including replicates) and over 100,000 pairwise comparisons. As each individual chromosomal substitution strain represents on average less than a 5% change from the parental genome, consomic strains provide a useful mechanism to dissect complex traits and identify causative genes. We performed a variety of data-mining manipulations on the profiles and used complementary physiological data from the PhysGen resource to demonstrate how TREX can be used by the cardiovascular community for hypothesis generation.
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