title: Physiogenomic resources for rat models of heart, lung and blood disorders.
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.
authors.affiliation: TREX, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
authors.forename: Renae L
authors.initials: RL
authors.lastname: Malek
authors.forename: Hong-ying
authors.initials: HY
authors.lastname: Wang
authors.forename: Anne E
authors.initials: AE
authors.lastname: Kwitek
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Greene
authors.forename: Nirmal
authors.initials: N
authors.lastname: Bhagabati
authors.forename: Gretta
authors.initials: G
authors.lastname: Borchardt
authors.forename: Lisa
authors.initials: L
authors.lastname: Cahill
authors.forename: Tracey
authors.initials: T
authors.lastname: Currier
authors.forename: Bryan
authors.initials: B
authors.lastname: Frank
authors.forename: Xianping
authors.initials: X
authors.lastname: Fu
authors.forename: Michael
authors.initials: M
authors.lastname: Hasinoff
authors.forename: Eleanor
authors.initials: E
authors.lastname: Howe
authors.forename: Noah
authors.initials: N
authors.lastname: Letwin
authors.forename: Truong V
authors.initials: TV
authors.lastname: Luu
authors.forename: Alexander
authors.initials: A
authors.lastname: Saeed
authors.forename: Hedieh
authors.initials: H
authors.lastname: Sajadi
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Razvan
authors.initials: R
authors.lastname: Sultana
authors.forename: Mathangi
authors.initials: M
authors.lastname: Thiagarajan
authors.forename: Jennifer
authors.initials: J
authors.lastname: Tsai
authors.forename: Kathleen
authors.initials: K
authors.lastname: Veratti
authors.forename: Joseph
authors.initials: J
authors.lastname: White
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Howard J
authors.initials: HJ
authors.lastname: Jacob
authors.forename: Norman H
authors.initials: NH
authors.lastname: Lee
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D004195:Disease Models, Animal; D020869:Gene Expression Profiling; D014644:Genetic Variation; D023281:Genomics / Q000379:methods; D006331:Heart Diseases / Q000235:genetics* / Q000503:physiopathology; D006402:Hematologic Diseases / Q000235:genetics* / Q000503:physiopathology; D000860:Hypoxia / Q000139:chemically induced; D020407:Internet; D008171:Lung Diseases / Q000235:genetics* / Q000503:physiopathology; D008297:Male; D046228:Microarray Analysis; D009206:Myocardium / Q000378:metabolism; D051381:Rats; D011914:Rats, Inbred BN; D020303:Rats, Inbred Dahl; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics