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Running head: Dissecting tBHQ induced ARE driven gene expression
BibTeX
@MISC{Li_runninghead:,
author = {Jiang Li and Maria L. Spletter and Jeffrey A. Johnson and Corresponding Jeffrey},
title = {Running head: Dissecting tBHQ induced ARE driven gene expression},
year = {}
}
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Abstract
Copyright © 2004 by the American Physiological Society. PG-00214-2004 FINAL ACCEPTED VERSION This paper compares the gene expression profiles identified by short (Affymetrix U95AV2) or long (Agilent Hu1A) oligonucleotide arrays on a model for upregulation of a cluster of antioxidant responsive element-driven genes by treatment with tert-butylhydroquinone. MAS5.0, dCHIP, and RMA were applied to normalize the Affymetrix data while Lowess Regression was considered for Agilent data. SAM was used to identify the differential gene expression. A set of biological markers and housekeeping genes were chosen to evaluate the performance of multiple normalization approaches. Both arrays illustrated a definite set of overlapping genes between the datasets regardless of data mining tools used. However, unique gene expression profiles based on the platform used also were revealed and confirmed by quantitative RT-PCR. Further analysis of the data revealed by alternative approaches suggested that alternative splicing, multiple vs. single probe(s) measurement, and use or nonuse of mismatch probes may account for the discrepant data. Therefore, these two microarray technologies offer relatively reliable data. Integration of the gene expression profiles from different array platforms may not only help for cross validation but also provide a more complete view of the transcriptional scenario.
Keyphrases
driven gene expression dissecting tbhq gene expression profile pg-00214-2004 final accepted version antioxidant responsive element-driven gene transcriptional scenario quantitative rt-pcr reliable data single probe agilent data unique gene expression profile discrepant data multiple v biological marker cross validation american physiological society data mining tool agilent hu1a alternative splicing mismatch probe complete view definite set multiple normalization approach microarray technology affymetrix data different array platform alternative approach lowess regression affymetrix u95av2 differential gene expression
