JCVI: Physiogenomic Resources for Rat Models of Heart, Lung and Blood Disorders
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Malek, R. L., Wang, H. Y., Kwitek, A. E., Greene, A. S., Bhagabati, N., Borchardt, G., Cahill, L., Currier, T., Frank, B., Fu, X., Hasinoff, M., Howe, E., Letwin, N., Luu, T. V., Saeed, A., Sajadi, H., Salzberg, S. L., Sultana, R., Thiagarajan, M., Tsai, J., Veratti, K., White, J., Quackenbush, J., Jacob, H. J., Lee, N. H.

Physiogenomic Resources for Rat Models of Heart, Lung and Blood Disorders

Nat Genet. 2006 Jan 15; 38(2): 234-9.

PubMed Citation


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.