Three microarray platforms: an analysis of their concordance in profiling gene expression.
BACKGROUND
Microarrays for the analysis of gene expression are of three different types: short oligonucleotide (25-30 base), long oligonucleotide (50-80 base), and cDNA (highly variable in length). The short oligonucleotide and cDNA arrays have been the mainstay of expression analysis to date, but long oligonucleotide platforms are gaining in popularity and will probably replace cDNA arrays. As part of a validation study for the long oligonucleotide arrays, we compared and contrasted expression profiles from the three formats, testing RNA from six different cell lines against a universal reference standard.


RESULTS
The three platforms had 6430 genes in common. In general, correlation of gene expression levels across the platforms was good when defined by concordance in the direction of expression difference (upregulation or downregulation), scatter plot analysis, principal component analysis, cell line correlation or quantitative RT-PCR. The overall correlations (r values) between platforms were in the range 0.7 to 0.8, as determined by analysis of scatter plots. When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%.


CONCLUSIONS
Our results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties. All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.
Petersen
David
D
Advanced Technology Center, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD 20877, USA. petersed@mail.nih.gov
Chandramouli
G V R
GV
Geoghegan
Joel
J
Hilburn
Joanne
J
Paarlberg
Jonathon
J
Kim
Chang Hee
CH
Munroe
David
D
Gangi
Lisa
L
Han
Jing
J
Puri
Raj
R
Staudt
Lou
L
Weinstein
John
J
Barrett
J Carl
JC
Green
Jeffrey
J
Kawasaki
Ernest S
ES
D002460:Cell Line; D016000:Cluster Analysis; D015342:DNA Probes; D018076:DNA, Complementary / Q000378:metabolism; D015536:Down-Regulation; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D015723:Gene Library; D015894:Genome, Human; D006801:Humans; D007091:Image Processing, Computer-Assisted; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015854:Up-Regulation
D015342:DNA Probes; D018076:DNA, Complementary; D015345:Oligonucleotide Probes; D009841:Oligonucleotides