A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.
Over the last decade, gene expression microarrays have had a profound impact on biomedical research. The diversity of platforms and analytical methods available to researchers have made the comparison of data from multiple platforms challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and 'in-house' platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by quantitative real-time (QRT)-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
Kuo
Winston Patrick
WP
Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave., Boston, Massachusetts 02115, USA. wkuo@genetics.med.harvard.edu
Liu
Fang
F
Trimarchi
Jeff
J
Punzo
Claudio
C
Lombardi
Michael
M
Sarang
Jasjit
J
Whipple
Mark E
ME
Maysuria
Malini
M
Serikawa
Kyle
K
Lee
Sun Young
SY
McCrann
Donald
D
Kang
Jason
J
Shearstone
Jeffrey R
JR
Burke
Jocelyn
J
Park
Daniel J
DJ
Wang
Xiaowei
X
Rector
Trent L
TL
Ricciardi-Castagnoli
Paola
P
Perrin
Steven
S
Choi
Sangdun
S
Bumgarner
Roger
R
Kim
Ju Han
JH
Short
Glenn F
GF
Freeman
Mason W
MW
Seed
Brian
B
Jensen
Roderick
R
Church
George M
GM
Hovig
Eivind
E
Cepko
Connie L
CL
Park
Peter
P
Ohno-Machado
Lucila
L
Jenssen
Tor-Kristian
TK
D002874:Chromosome Mapping / Q000379:methods*; D015342:DNA Probes / Q000737:chemistry / Q000145:classification; D020869:Gene Expression Profiling / Q000379:methods*; D046228:Microarray Analysis / Q000145:classification / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results
D015342:DNA Probes