Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells.
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.
Lee
Jae K
JK
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-8322, USA. jaeklee@virginia.edu
Bussey
Kimberly J
KJ
Gwadry
Fuad G
FG
Reinhold
William
W
Riddick
Gregory
G
Pelletier
Sandra L
SL
Nishizuka
Satoshi
S
Szakacs
Gergely
G
Annereau
Jean-Phillipe
JP
Shankavaram
Uma
U
Lababidi
Samir
S
Smith
Lawrence H
LH
Gottesman
Michael M
MM
Weinstein
John N
JN
D000465:Algorithms; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*