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

doi:10.1186/gb-2003-4-12-r82

Genome Biology

Volume 4
Issue 12

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Lee JK
Bussey KJ
Gwadry FG
Reinhold W
Riddick G
Pelletier SL
Nishizuka S
Szakacs G
Annereau JP
Shankavaram U
Lababidi S
Smith LH
Gottesman MM
Weinstein JN

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Lee JK
Bussey KJ
Gwadry FG
Reinhold W
Riddick G
Pelletier SL
Nishizuka S
Szakacs G
Annereau JP
Shankavaram U
Lababidi S
Smith LH
Gottesman MM
Weinstein JN
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Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells

Jae K Lee¹^,3 , Kimberly J Bussey¹, Fuad G Gwadry¹, William Reinhold¹, Gregory Riddick³, Sandra L Pelletier³, Satoshi Nishizuka¹, Gergely Szakacs², Jean-Phillipe Annereau², Uma Shankavaram¹, Samir Lababidi¹, Lawrence H Smith¹, Michael M Gottesman² and John N Weinstein¹

¹Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-8322, USA

²Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-8322, USA

³Current address: Department of Health Evaluation Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA

author email corresponding author email

Genome Biology 2003, 4:R82doi:10.1186/gb-2003-4-12-r82


Published:	25 November 2003

Subject areas: Genetics, Genome studies, Cancer, Methods, Bioinformatics

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.