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Originally published In Press as doi:10.1074/mcp.M400055-MCP200 on July 6, 2004.
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Molecular & Cellular Proteomics 3:960-969, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells*,S

Qiang Tian{ddagger},§,¶, Serguei B. Stepaniants||,§,¶, Mao Mao||,§, Lee Weng||, Megan C. Feetham{ddagger}, Michelle J. Doyle{ddagger}, Eugene C. Yi{ddagger}, Hongyue Dai||, Vesteinn Thorsson{ddagger}, Jimmy Eng{ddagger}, David Goodlett{ddagger}, Joel P. Berger||, Bert Gunter||, Peter S. Linseley||, Roland B. Stoughton||, Ruedi Aebersold{ddagger}, Steven J. Collins**, William A. Hanlon|| and Leroy E. Hood{ddagger}

From the {ddagger} The Institute for Systems Biology, Seattle, WA 98103; || Rosetta Inpharmatics, Merck Research Laboratories, Seattle, WA 98109; ** Fred Hutchinson Cancer Research Center, Human Biology Division, Seattle, WA 98125

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.

To whom correspondence should be addressed: Qiang Tian, Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904. Tel.: 206-732-1308; Fax: 206-732-1299; E-mail: qtian{at}systemsbiology.org. Serguei B. Stepaniants, Rosetta Inpharmatics, 401 Terry Avenue North, Seattle, WA 98109. Tel.: 206-802-7348; Fax: 206-802-6411; E-mail: serguei_stepaniants{at}merck.com


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