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Hybridization Dynamics Compensation in Microarray Experiments

  • Raul Malutan
  • Pedro Gómez Vilda
  • Ioana Berindan Neagoe
  • Monica Borda
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 93)

Abstract

The dynamics of the hybridization process in microarrays experiments is complex as thermodynamics factors influencing molecular interaction are still fields of important research and their effects are not fully taken into account in the estimation of genetic expression. In this paper an adaptive fitting is used to predict and regress microarray expression levels on a specific test probe to common thermodynamic conditions.

Keywords

hybridization microarray regression 

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References

  1. 1.
    Burden, C., Pittelkow, Y.E., Wilson, S.R.: Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays. Statistical Applications in Genetics and Molecular Biology 3(1), article 35 (2004)Google Scholar
  2. 2.
    Center for the Study of Biological Complexity, http://www.vcu.edu/csbc/
  3. 3.
    Dai, H., Meyer, M., Stepaniants, S., Ziman, M., Stoughton, R.: Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Research 30(16), e86.1 – e86.8 (2002)CrossRefGoogle Scholar
  4. 4.
    Diaz, F., et al.: Estimating Oligo-nucleotide Microarray Expression by Hybridization Process Modelling. In: IEEE/NLM Life Science Systems and Applications Workshop (2006), doi:10.1109/LSSA.2006.250398Google Scholar
  5. 5.
    El Samad, H., Khammash, M., Petzold, L., Gillespie, D.: Stochastic Modelling of Gene Regulatory Networks. Int. Journal of Robust and Nonlinear Control 15(15), 691–711 (2005)zbMATHCrossRefGoogle Scholar
  6. 6.
    Malutan, R., Gómez, P., Borda, M.: Oligonucleotide Microarray Probe Correction by FixedPoint ICA Algorithm. In: Omatu, S., Rocha, M.P., Bravo, J., Fernández, F., Corchado, E., Bustillo, A., Corchado, J.M. (eds.) IWANN 2009. LNCS, vol. 5518, pp. 988–991. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  7. 7.
    Malutan, R., Gómez, P., Borda, M.: Independent component analysis algorithms for microarray data analysis. Intelligent Data Analysis Journal 14(2), 193–206 (2010)Google Scholar
  8. 8.
    Sugimoto, N., et al.: Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Research 24(22), 4501–4505 (1996)CrossRefGoogle Scholar
  9. 9.
    Zhang, L., Miles, M.F., Aldape, K.D.: A model of molecular interactions on short oligonucleotide microarrays. Nature Biotechnology 21(7), 818–821 (2003)CrossRefGoogle Scholar
  10. 10.
    Zhang, Y., Hammer, D.A., Graves, D.J.: Competitive Hybridization Kinetics Reveals Unexpected Behavior Patterns. Biophysical Journal 89, 2950–2959 (2005)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Raul Malutan
    • 1
  • Pedro Gómez Vilda
    • 2
  • Ioana Berindan Neagoe
    • 3
  • Monica Borda
    • 1
  1. 1.Technical University of Cluj-NapocaCluj-NapocaRomania
  2. 2.Universidad Politécnica de MadridMadridSpain
  3. 3.The Oncology Institute “Prof. Dr. Ion Chiricuta”Cluj-NapocaRomania

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