Integrated genomic and proteomic analyses of gene expression in mammalian cells

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

Research output: Contribution to journalArticlepeer-review

664 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)960-969
Number of pages10
JournalMolecular and Cellular Proteomics
Issue number10
StatePublished - Oct 2004


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