Dissecting tBHQ induced ARE-driven gene expression through long and short oligonucleotide arrays
Open Access
- 21 March 2005
- journal article
- Published by American Physiological Society in Physiological Genomics
- Vol. 21 (1) , 43-58
- https://doi.org/10.1152/physiolgenomics.00214.2004
Abstract
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.Keywords
This publication has 58 references indexed in Scilit:
- Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarraysBioinformatics, 2004
- Evaluation of gene expression measurements from commercial microarray platformsNucleic Acids Research, 2003
- Spotted Long Oligonucleotide Arrays for Human Gene Expression AnalysisGenome Research, 2003
- Control Genes and Variability: Absence of Ubiquitous Reference Transcripts in Diverse Mammalian Expression StudiesGenome Research, 2002
- Gene expression profiling predicts clinical outcome of breast cancerNature, 2002
- Significance analysis of microarrays applied to the ionizing radiation responseProceedings of the National Academy of Sciences, 2001
- Initial sequencing and analysis of the human genomeNature, 2001
- Thioredoxin reductase and glutathione synthesis is upregulated byt-butylhydroquinone in cortical astrocytes but not in cortical neuronsGlia, 2000
- Up-Regulation of the Human γ-Glutamylcysteine Synthetase Regulatory Subunit Gene Involves Binding of Nrf-2 to an Electrophile Responsive ElementBiochemical and Biophysical Research Communications, 1999
- Identification of a Putative Antioxidant Response Element in the 5′-Flanking Region of the Human γ-Glutamylcysteine Synthetase Heavy Subunit GeneBiochemical and Biophysical Research Communications, 1995