Transcript and protein expression profiles of the NCI-60 cancer cell panel: An integromic microarray study

Uma T. Shankavaram, William C. Reinhold, Satoshi Nishizuka, Sylvia Major, Daisaku Morita, Krishna K. Chary, Mark A. Reimers, Uwe Scherf, Ari Kahn, Douglas Dolginow, Jeffrey Cossman, Eric P. Kaldjian, Dominic A. Scudiero, Emanuel Petricoin, Lance Liotta, Jae K. Lee, John N. Weinstein*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

270 Scopus citations


To evaluate the utility of transcript profiling for prediction of protein expression levels, we compared profiles across the NCI-60 cancer cell panel, which represents nine tissues of origin. For that analysis, we present here two new NCI-60 transcript profile data sets (A based on Affymetrix HG-U95 and HG-U133A chips; Affymetrix, Santa Clara, CA) and one new protein profile data set (based on reverse-phase protein lysate arrays). The data sets are available online at in the CellMiner program package. Using the new transcript data in combination with our previously published cDNA array and Affymetrix HU6800 data sets, we first developed a "consensus set" of transcript profiles based on the four different microarray platforms. Using that set, we found that 65% of the genes showed statistically significant transcript-protein correlation, and the correlations were generally higher than those reported previously for panels of mammalian cells. Using the predictive analysis of microarray nearest shrunken centroid algorithm for functional prediction of tissue of origin, we then found that (a) the consensus mRNA set did better than did data from any of the individual mRNA platforms and (b) the protein data seemed to do somewhat better (P = 0.027) on a gene-for-gene basis in this particular study than did the consensus mRNA data, but both did well. Analysis based on the Gene Ontology showed protein levels of structure-related genes to be well predicted by mRNA levels (mean r = 0.71). Because the transcript-based technologies are more mature and are currently able to assess larger numbers of genes at one time, they continue to be useful, even when the ultimate aim is information about proteins.

Original languageEnglish
Pages (from-to)820-832
Number of pages13
JournalMolecular Cancer Therapeutics
Issue number3
StatePublished - Mar 2007
Externally publishedYes


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