Physiogenomic resources for rat models of heart, lung and blood disorders

RL Malek, H Wang, AE Kwitek, AS Greene… - Nature …, 2006 - nature.com
RL Malek, H Wang, AE Kwitek, AS Greene, N Bhagabati, G Borchardt, L Cahill, T Currier…
Nature genetics, 2006nature.com
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 …
Abstract
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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