Physiogenomic resources for rat models of heart, lung and blood disorders.
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.
Malek
Renae L
RL
TREX, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
Wang
Hong-ying
HY
Kwitek
Anne E
AE
Greene
Andrew S
AS
Bhagabati
Nirmal
N
Borchardt
Gretta
G
Cahill
Lisa
L
Currier
Tracey
T
Frank
Bryan
B
Fu
Xianping
X
Hasinoff
Michael
M
Howe
Eleanor
E
Letwin
Noah
N
Luu
Truong V
TV
Saeed
Alexander
A
Sajadi
Hedieh
H
Salzberg
Steven L
SL
Sultana
Razvan
R
Thiagarajan
Mathangi
M
Tsai
Jennifer
J
Veratti
Kathleen
K
White
Joseph
J
Quackenbush
John
J
Jacob
Howard J
HJ
Lee
Norman H
NH
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