Abstract
The newly developed microarray technology has made it possible to simultaneously monitor the expression of thousands of genes under specific physiological and pathological conditions. An array contains thousands of nucleic acid probes with known sequences. When the labeled target nucleic acid is applied to the array, it hybridizes to the probe if their sequences are complimentary to each other. The hybridization can be measured and the gene expression level estimated.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Shi, L. (2002) DNA Microarray (Genome Chip)—Monitoring the Genome on a Chip, http://www.gene-chips.com.
Buhler, J. (2001) Anatomy of a comparative gene expression study, http://www.cs.wustl.edu/~jbuhler//research/array/.
Quackenbush, J. (2001) Computational analysis of microarray data. Nature Rev. Genet. 2, 418–427.
Wu, T. D. (2001) Analysing gene expression data from DNA microarrays to identify candidate genes. J. Pathol. 195, 53–65.
Tong, L., Shen, H., Perreau, V. M., et al. (2001) Effects of exercise on geneexpression profile in the rat hippocampus. Neurobiol. Dis. 8, 1046–1056.
Schadt, E. E., Li, C., Ellis, B., and Wong, W. H. (2001) Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell. Biochem. 37(Suppl.), 120–125.
DeRisi, J., Penland, L., Brown, P. O., et al. (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genet. 14, 457–460.
Schena, M., Shalon, D., Davis, R. W., et al. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.
Schena, M., Shalon, D., Heller, R., et al. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93, 10,614–10,619.
Affymetrix (2001) Statistical Algorithms Reference Guide, Technical Report, Affymetrix, Santa Clara, CA.
Hakak, Y., Walker, J. R., Li, C., et al. (2001) Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proc. Natl. Acad. Sci. USA 98, 4746–4751.
Bouton, C. M. L. S., Hossain, M. A., Frelin, L. P., et al. (2001) Microarray analysis of differential gene expression in lead-exposed astrocytes. Toxicol. Appl. Pharmacol. 176, 34–53.
Liu, J., Chen, H., Miller, D. S., et al. (2001) Overexpression of glutathione S-transferase II and multidrug resistance transport proteins is associated with acquired tolerance to inorganic arsenic. Mol. Pharmacol. 60, 302–309.
Richer, J. K., Jacobsen, B. M., Manning, N. G., et al. (2002) Differential gene regulation by the two progesterone receptor isoforms in human breast cancer cells. J. Biol. Chem. 277, 5209–5218.
Westfall, P. H. and Young, S. S. (1993) Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment, Wiley, New York.
Dudoit, S., Yang, Y. H., Callow, M. J., et al. (2000) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments, http://www.stat.berkeley.edu/users/terry/zarray/TechReport/578.pdf.
Tusher, V. G., Tibshirani, R., and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116–5121.
Johnson, R. and Wichern, D. W. (1988) Applied Multivariate Statistical Analysis, Prentice-Hall, Englewood Cliffs, NJ.
Kohonen, T. (1995) Self-Organizing Maps, Springer-Verlag, Berlin.
Xie, T., Tong, L., Barrett, T., et al. (2002) Changes in gene expression linked to methamphetamine-induced dopaminergic neurotoxicity. J. Neurosci. 22, 274–283.
Li, C. and Wong, W. H. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98, 31–36.
Li, C. and Wong, W. H. (2001) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, 1–11.
Hornik, K. (2002) The R FAQ, http://www.r-project.org.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Hu, D. (2003). Microarray Data Analysis in Studies of Membrane Transporters. In: Yan, Q. (eds) Membrane Transporters. Methods in Molecular Biology, vol 227. Humana Press. https://doi.org/10.1385/1-59259-387-9:71
Download citation
DOI: https://doi.org/10.1385/1-59259-387-9:71
Publisher Name: Humana Press
Print ISBN: 978-1-58829-104-2
Online ISBN: 978-1-59259-387-3
eBook Packages: Springer Protocols