title: Consistency of predictive signature genes and classifiers generated using different microarray platforms.
abstract: Microarray-based classifiers and associated signature genes generated from various platforms are abundantly reported in the literature; however, the utility of the classifiers and signature genes in cross-platform prediction applications remains largely uncertain. As part of the MicroArray Quality Control Phase II (MAQC-II) project, we show in this study 80-90% cross-platform prediction consistency using a large toxicogenomics data set by illustrating that: (1) the signature genes of a classifier generated from one platform can be directly applied to another platform to develop a predictive classifier; (2) a classifier developed using data generated from one platform can accurately predict samples that were profiled using a different platform. The results suggest the potential utility of using published signature genes in cross-platform applications and the possible adoption of the published classifiers for a variety of applications. The study reveals an opportunity for possible translation of biomarkers identified using microarrays to clinically validated non-array gene expression assays.
authors.affiliation: College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
authors.forename: X
authors.initials: X
authors.lastname: Fan
authors.forename: E K
authors.initials: EK
authors.lastname: Lobenhofer
authors.forename: M
authors.initials: M
authors.lastname: Chen
authors.forename: W
authors.initials: W
authors.lastname: Shi
authors.forename: J
authors.initials: J
authors.lastname: Huang
authors.forename: J
authors.initials: J
authors.lastname: Luo
authors.forename: J
authors.initials: J
authors.lastname: Zhang
authors.forename: S J
authors.initials: SJ
authors.lastname: Walker
authors.forename: T-M
authors.initials: TM
authors.lastname: Chu
authors.forename: L
authors.initials: L
authors.lastname: Li
authors.forename: R
authors.initials: R
authors.lastname: Wolfinger
authors.forename: W
authors.initials: W
authors.lastname: Bao
authors.forename: R S
authors.initials: RS
authors.lastname: Paules
authors.forename: P R
authors.initials: PR
authors.lastname: Bushel
authors.forename: J
authors.initials: J
authors.lastname: Li
authors.forename: T
authors.initials: T
authors.lastname: Shi
authors.forename: T
authors.initials: T
authors.lastname: Nikolskaya
authors.forename: Y
authors.initials: Y
authors.lastname: Nikolsky
authors.forename: H
authors.initials: H
authors.lastname: Hong
authors.forename: Y
authors.initials: Y
authors.lastname: Deng
authors.forename: Y
authors.initials: Y
authors.lastname: Cheng
authors.forename: H
authors.initials: H
authors.lastname: Fang
authors.forename: L
authors.initials: L
authors.lastname: Shi
authors.forename: W
authors.initials: W
authors.lastname: Tong
mesh_terms: D000465:Algorithms; D000818:Animals; D015342:DNA Probes; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005796:Genes; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010597:Pharmacogenetics / Q000379:methods*; D010641:Phenotype; D011237:Predictive Value of Tests; D011786:Quality Control; D043922:Toxicogenetics / Q000379:methods*
chemical_list: D015342:DNA Probes