Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells.

Jae K. Lee, Kimberly J. Bussey, Fuad G. Gwadry, William Reinhold, Gregory Riddick, Sandra L. Pelletier, Satoshi Nishizuka, G. Szakács, Jean Phillipe Annereau, Uma Shankavaram, Samir Lababidi, Lawrence H. Smith, Michael M. Gottesman, John N. Weinstein

Research output: Contribution to journalArticle

93 Citations (Scopus)

Abstract

Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. We describe here a different approach based on simultaneous mutual validation of large numbers of genes using two different expression-profiling platforms. The result described here for the NCI-60 cancer cell lines is a consensus set of genes that give similar profiles on spotted cDNA arrays and Affymetrix oligonucleotide chips. Global concordance is parameterized by a 'correlation of correlations' coefficient.

Original languageEnglish
JournalGenome Biology
Volume4
Issue number12
Publication statusPublished - 2003

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oligonucleotides
Oligonucleotide Array Sequence Analysis
gene expression
cancer
Gene Expression
gene
Genes
Neoplasms
genes
Transcriptome
Oligonucleotides
Real-Time Polymerase Chain Reaction
reverse transcriptase polymerase chain reaction
cell lines
Cell Line
neoplasm cells

ASJC Scopus subject areas

  • Genetics

Cite this

Lee, J. K., Bussey, K. J., Gwadry, F. G., Reinhold, W., Riddick, G., Pelletier, S. L., ... Weinstein, J. N. (2003). Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biology, 4(12).

Comparing cDNA and oligonucleotide array data : concordance of gene expression across platforms for the NCI-60 cancer cells. / Lee, Jae K.; Bussey, Kimberly J.; Gwadry, Fuad G.; Reinhold, William; Riddick, Gregory; Pelletier, Sandra L.; Nishizuka, Satoshi; Szakács, G.; Annereau, Jean Phillipe; Shankavaram, Uma; Lababidi, Samir; Smith, Lawrence H.; Gottesman, Michael M.; Weinstein, John N.

In: Genome Biology, Vol. 4, No. 12, 2003.

Research output: Contribution to journalArticle

Lee, JK, Bussey, KJ, Gwadry, FG, Reinhold, W, Riddick, G, Pelletier, SL, Nishizuka, S, Szakács, G, Annereau, JP, Shankavaram, U, Lababidi, S, Smith, LH, Gottesman, MM & Weinstein, JN 2003, 'Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells.', Genome Biology, vol. 4, no. 12.
Lee, Jae K. ; Bussey, Kimberly J. ; Gwadry, Fuad G. ; Reinhold, William ; Riddick, Gregory ; Pelletier, Sandra L. ; Nishizuka, Satoshi ; Szakács, G. ; Annereau, Jean Phillipe ; Shankavaram, Uma ; Lababidi, Samir ; Smith, Lawrence H. ; Gottesman, Michael M. ; Weinstein, John N. / Comparing cDNA and oligonucleotide array data : concordance of gene expression across platforms for the NCI-60 cancer cells. In: Genome Biology. 2003 ; Vol. 4, No. 12.
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