Abstract
A DNA microarray consists of an orderly arrangement of DNA, cDNA, or oligonucleotide probes that represent individual genes of an organism. Today, microarrays are the most important tools used to analyze gene transcription on a large scale. Investigations reach from finding key genes in whole genomes to looking at overall patterns of gene expression. This provides a better understanding of the architecture of genetic regulatory networks and helps to identify those genes in the genome that are differentially expressed, e.g., during cellular programs, in tumors or as the result of a treatment. The use of different fluorescent dyes allows mRNAs from two different sources (tissues, strains, or differently treated cells) to be labeled in different colors, mixed, and hybridized to the same array, which results in competitive binding of the target to the arrayed sequences. After hybridization and washing, the slide is scanned using two different wavelengths corresponding to the dyes used, and the intensity of the same spot in both channels is compared. This results in a measurement of the ratio of transcript levels for each gene represented on the array. In order to find significantly regulated genes, the resulting data are analyzed by different bioinformatic tools such as R and significance analysis of microarrays (SAM).
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Schulze, A. and Downward, J. (2001) Navigating gene expression using micro-arrays—a technology review. Nat. Cell Biol. 3, E190–E195.
Schena, M., Shalon, D., Davis, R.W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.
Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. O., and Davis, R. W. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93, 10,614–10,619.
Shalon, D., Smith, S. J., and Brown, P. O. (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639–645.
Lipshutz, R. J., Morris, D., Chee, M., et al. (1995) Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 19, 442–447.
Lipshutz, R. J., Fodor, S. P., Gingeras, T. R., and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20–24.
Duggan, D. J., Bittner, M., Chen, Y., Meltzer, P., and Trent, J. M. (1999) Expression profiling using cDNA microarrays. Nat. Genet. 21, 10–14.
Kwast, K. E., Lai, L. C., Menda, N., James, D. T., 3rd, Aref, S., and Burke, P. V. (2002) Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response. J. Bacteriol. 184, 250–265.
DeRisi, J., Penland, L., Brown, P. O., et al. (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14, 457–460.
Heller, R. A., Schena, M., Chai, A., et al. (1997) Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc. Natl. Acad. Sci. USA 94, 2150–2155.
Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14,863–14,868.
Van Driessche, N., Shaw, C., Katoh, M., et al. (2002) A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 129, 1543–1552.
Dyrskjot, L. (2003) Classification of bladder cancer by microarray expression profiling: towards a general clinical use of microarrays in cancer diagnostics. Expert. Rev. Mol. Diagn. 3, 635–647.
Kibler, K., Nguyen, T. L., Svetz, J., et al. (2003) A novel developmental mechanism in Dictyostelium revealed in a screen for communication mutants. Dev. Biol. 259, 193–208.
Girardot, F., Monnier, V., and Tricoire, H. (2004) Genome wide analysis of common and specific stress responses in adult Drosophila melanogaster. BMC Genomics 5, 74.
Spellman, P. T., Sherlock, G., Zhang, M. Q., et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273–3297.
Urushihara, H., Morio, T., Saito, T., et al. (2004) Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum. Nucleic Acids Res. 32, 1647–1653.
Eichinger, L., Pachebat, J. A., Glockner, G., et. al. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43–57.
Dudoit, S., Yang, Y. H., and Bolstad, B. (2002) Using R for the analysis of DNA microarray data. R News 2, 24–32.
Dudoit, S. and Yang, Y. H. (2003) Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data, in The Analysis of Gene Expression Data: Methods and Software (Zeger, S. L., ed.). Springer, New York: pp. 455–468.
Bland, J. M. and Altman, D. G. (1986) Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1, 307–310.
Smyth, G. K., Yang, Y. H., and Speed, T. (eds.) (2002) Statistical issues in cDNA Microarray Data Analysis, in Functional Genomics (Brownstein, M. J. and Khodursky, A., eds.). Humana Press, Totowa: pp. 111–136.
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.
Martinez, M. J., Aragon, A. D., Rodriguez, A. L., et al. (2003) Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays. Nucleic Acids Res. 31, E18.
Yang, Y. H. and Speed, T. (2002) Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3, 579–588.
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Kaul, M., Eichinger, L. (2006). Analysis of Gene Expression Using cDNA Microarrays. In: Eichinger, L., Rivero, F. (eds) Dictyostelium discoideum Protocols. Methods in Molecular Biology™, vol 346. Humana Press. https://doi.org/10.1385/1-59745-144-4:75
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DOI: https://doi.org/10.1385/1-59745-144-4:75
Publisher Name: Humana Press
Print ISBN: 978-1-58829-623-8
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