HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

Physiol. Genomics 21: 43-58, 2005. First published December 21, 2004; doi:10.1152/physiolgenomics.00214.2004
1094-8341/05 $8.00

This Article Free upon publication Full Text Full Text (PDF) Supplemental Material All Versions of this Article: 21/1/43    most recent 00214.2004v1 Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Web of Science (3) Citing Articles via Google Scholar Google Scholar Articles by Li, J. Articles by Johnson, J. A. Search for Related Content PubMed PubMed Citation Articles by Li, J. Articles by Johnson, J. A.

Dissecting tBHQ induced ARE-driven gene expression through long and short oligonucleotide arrays

¹ School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin
² Environmental Toxicology Center, University of Wisconsin-Madison, Madison, Wisconsin
³ Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin

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. MAS 5.0, dCHIP, and RMA were applied to normalize the Affymetrix data, and 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 data sets regardless of data mining tools used. However, unique gene expression profiles based on the platform used were also 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.

microarray; cross-platform comparison; antioxidant responsive element; tert-butylhydroquinone

This article has been cited by other articles:

				M. Barnes, J. Freudenberg, S. Thompson, B. Aronow, and P. Pavlidis Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms Nucleic Acids Res., October 19, 2005; 33(18): 5914 - 5923. [Abstract] [Full Text] [PDF]

				S. H. Ahmed, R. Lutjens, L. D. van der Stap, D. Lekic, V. Romano-Spica, M. Morales, G. F. Koob, V. Repunte-Canonigo, and P. P. Sanna Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction PNAS, August 9, 2005; 102(32): 11533 - 11538. [Abstract] [Full Text] [PDF]