Integrated genomic and proteomic analyses of gene expression in Mammalian cells.
Using DNA microarrays together with quantitative proteomic techniques (ICAT reagents, two-dimensional DIGE, and MS), we evaluated the correlation of mRNA and protein levels in two hematopoietic cell lines representing distinct stages of myeloid differentiation, as well as in the livers of mice treated for different periods of time with three different peroxisome proliferative activated receptor agonists. We observe that the differential expression of mRNA (up or down) can capture at most 40% of the variation of protein expression. Although the overall pattern of protein expression is similar to that of mRNA expression, the incongruent expression between mRNAs and proteins emphasize the importance of posttranscriptional regulatory mechanisms in cellular development or perturbation that can be unveiled only through integrated analyses of both proteins and mRNAs.
Tian
Qiang
Q
The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA. qtian@systemsbiology.org
Stepaniants
Serguei B
SB
Mao
Mao
M
Weng
Lee
L
Feetham
Megan C
MC
Doyle
Michelle J
MJ
Yi
Eugene C
EC
Dai
Hongyue
H
Thorsson
Vesteinn
V
Eng
Jimmy
J
Goodlett
David
D
Berger
Joel P
JP
Gunter
Bert
B
Linseley
Peter S
PS
Stoughton
Roland B
RB
Aebersold
Ruedi
R
Collins
Steven J
SJ
Hanlon
William A
WA
Hood
Leroy E
LE
D000818:Animals; D002460:Cell Line; D017077:Culture Media, Conditioned; D015180:Electrophoresis, Gel, Two-Dimensional; D005786:Gene Expression Regulation; D014644:Genetic Variation; D023281:Genomics; D006412:Hematopoietic Stem Cells / Q000166:cytology; D007700:Kinetics; D008099:Liver / Q000187:drug effects; D008297:Male; D013058:Mass Spectrometry; D051379:Mice; D008810:Mice, Inbred C57BL; D023461:Myeloid Progenitor Cells / Q000166:cytology; D038042:Myelopoiesis; D020411:Oligonucleotide Array Sequence Analysis; D047492:Peroxisome Proliferator-Activated Receptors / Q000819:agonists; D020025:Peroxisome Proliferators / Q000494:pharmacology; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis / Q000378:metabolism; D040901:Proteomics; D011743:Pyrimidines / Q000494:pharmacology; D012333:RNA, Messenger / Q000032:analysis / Q000378:metabolism; D000077154:Rosiglitazone; D045162:Thiazolidinediones / Q000494:pharmacology
D017077:Culture Media, Conditioned; D047492:Peroxisome Proliferator-Activated Receptors; D020025:Peroxisome Proliferators; D011506:Proteins; D011743:Pyrimidines; D012333:RNA, Messenger; D045162:Thiazolidinediones; D000077154:Rosiglitazone; C006253:pirinixic acid; C089946:2,4-thiazolidinedione