2,639
Views
18
CrossRef citations to date
0
Altmetric
Articles

DNA microarray analysis: Principles and clinical impact

&
Pages 271-287 | Published online: 04 Sep 2013

References

  • Mount DW. Bioinformatics: Sequence and genome analysis. Cold Spring Harbor, New York: Cold Spring Harbor laboratory Press; 2001.
  • Lesk AM. Introduction to bioinformatics. Oxford: Oxford University Press; 2002.
  • Campbell AM, Heyer U. Discovering genomics, proteomics and bioinformatics. San Francisco: Benjamin Cummings; 2002.
  • Gibas C, Jambeck P. Developing bioinformatics computer skills. Sebastopol: O’Reilly; 2001.
  • Schena M, Shalon D, Davis RW, Brown PO. Quantitave monitoring of gene expression patterns with a complementary DNA microarray. Science 20;1995; 270(5235):467–470.
  • DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 24 1997;278(5338):680–686.
  • Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays. Nature 15 2000;405(6788):827–836.
  • Young RA. Biomedical discovery with DNA arrays. Cell 2000; 102(1):9–15.
  • Zhang MQ. Large-scale gene expression data analysis: A new challenge to computational biologists. Genome Res 1999; 9(8):681–688.
  • Schimek MG, Wiltgen M. Microarray gene expression analysis basics for biometricians. Colloquium Biometryczne 2004; 34a:141–159.
  • Sherlock G, Hernandez-Boussard T, et al. The Stanford Microarray database. Nucleic Acids Res 2001;29: 152–155.
  • Tseng GC, Oh M, Roblin L, Liao JC, Wong WH. Issues in cDNA microarray filtering: Quality filtering, channel normal-ization, models of variations and assessment of gene effects. Nucleic Acids Res 2001;29:2549–2557.
  • Churchill GA. Fundamentals of experimental design for cDNA microarrays. Nat Genet 2002;32:490–495.
  • Yang YH, Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet 2002;3:579–588.
  • Kooperberg C, Fazzio TG, Delrow JJ, Tsukiyama T. Background correction for spotted DNA microarrays. J Comput Biol 2002;9:55–66.
  • Quackenbush J. Microarray data normalization and trans-formation. Nat Genet 2002;32:496–501.
  • Clarke PA, te Poele R, Wooster R, Workman P. Gene expression microarray analysis in cancer biology, pharma-cology and drug development: Progress and potential. Biochem Pharmacol 2001;62:1311–1336.
  • Claverie JM. Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet 1999;8(10):1821–1832.
  • Eisen MB, Paul TS, et al. Cluster analysis and display of genome-wide expression patterns. PNAS 1998;95: 14863–14868.
  • Sturn A, Quackenbush J, Trajanoski Z. Genesis: Cluster analysis of microarray data. Bioinformatics 2002;18: 207–208.
  • Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson J, Jr., Boguski MS, Lashkari D, Shalon D, Brown PO. The transcriptional program in response to human fibroblasts to serum. Science 1999;1; 283:83–87.
  • Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, Barker JL, Somogyi R. Large-scale temporal gene expression of central nervous system development. Proc Natl acad Sci USA 1998;6;95 (1):334–339.
  • Kohonen T, Hynninen J, Kangas J, Jaaksonen J. SOM_PAK. The Self-Organizing Map Program Package. Manual Version 3.1. Helsinki University of Technology. Laboratory of Computer and Information Science 1995.
  • Tamayo P, Slonim D, Merisov J, Zhu Q, Kitareewan S, Dmitrovsky E, Landers ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999;16;96 (6):2907–2912.
  • Brown MPS, Grundy WN, Lin D, Christianini N, Sugnet C, Ares Mjr., Haussler D. Support vector machine classification of microarray gene expression data. UCSC-CRL-99-9. Santa Cruz: Department of Computer Science, University of California; 1999.
  • Brown MPS, Grundy WN, Lin D, Christianini N, Sugnet C, Furey TS, Ares M, Jr., Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000;4;97(1): 262–267.
  • Gaasterland T, Bekiranov S. Making the most of microarray data. Nat Genet 2000;24(3):204–206.
  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235–242.
  • Guex N, Peitsch MC. SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modelling. Electrophoresis 1997;18:2714–2723.
  • D’Haeseleer P, Wen X, Fuhrman S, Somogyi R. Linear modelling of mRNA expression levels during CNS develop-ment and injury. In: Altman R, editor. Proceedings of the Pacific Symposium on Biocomputing. Singapore: World Scientific; 1999. p 41–52.
  • Somogyi R, Fuhrman S, Wen X. Genetic network inference in computational models and applications to large-scale gene expression data. In: Bower JM, Bolouri H, editors. Compu-tational modelling of genetic and biochemical networks. Cambridge, MA: MIT Press; 2001. p 119–157.
  • Friedman N, Linial M, Nachman I, Pe’er D. Using Bayesian networks to analyse expression data. J Comp Biol 2000;7: 601–620.
  • Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 1999; 96(12):6745–6750.
  • Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeck M, Merisov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 15 1999;286(5439): 531–537.
  • Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT, Pergamenschikov A, Williams CF, Zhu SX, Lee JC, Lashkari D, Shalon D, Brown PO, Botstein D. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 1999;3; 96(16):9212–9217.
  • Liotta L, Petricoin E. Molecular profiling of human cancer. Nat Rev Genet 2000;1:48–56.
  • Cooper CS. Applications of microarray technology in breast cancer research. Breast Cancer Res 2001;3: 158–175.
  • Spear B, Heath-Chiozzi M, Huff J. Clinical application of pharmacogenetics. Trends Mol Med 2001;7:201–204.
  • Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JL, Yang L, Marti GE, Moore T, Hudson J, Jr., Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM, et al. Distinct types of diffuse large B-cell lymhona identified by gene expression profiling. Nature 2000;3;403(6769): 503–511.
  • Galon J, Ccostes A, Sanchez-Cabo F, Kirilovsky A, Mlecnik B, Lagorce-Pages C, Tosolini M, Camus M, Berger A, Wind P, Zizindohoue F, Bruneval P, Cugnenc PH, Trajanoski Z, Fridman WH, Pages F. Type, density and location of immune cells within human colorectal tumors predict clinical outcome. Science 2006;313:1960–1964.
  • Pagliarulo V, Datar RH. Role of genetic and expression profiling in pharmacogenomics: The changing face of patient management. Curr Issues Mol Biol 2002;4: 101–110.
  • Chicurel ME, Dalma-Weiszhaus DD. Microarrays in pharma-cogenomics—advantages and future promise. Pharmacoge-nomics 2002;3:589–601.
  • Scherf U, Ross D, et al. A gene expression database for molecular pharmacology of cancer. Nature Genetics 2000;24: 236–244.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.