Skip to main content

Part of the book series: Advances in Intelligent and Soft Computing ((AINSC,volume 93))

  • 809 Accesses

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  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. Center for the Study of Biological Complexity, http://www.vcu.edu/csbc/

  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)

    Article  Google Scholar 

  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.2006.250398

    Google Scholar 

  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)

    Article  MATH  Google Scholar 

  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)

    Chapter  Google Scholar 

  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. 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)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  10. Zhang, Y., Hammer, D.A., Graves, D.J.: Competitive Hybridization Kinetics Reveals Unexpected Behavior Patterns. Biophysical Journal 89, 2950–2959 (2005)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Malutan, R., Vilda, P.G., Neagoe, I.B., Borda, M. (2011). Hybridization Dynamics Compensation in Microarray Experiments. In: Rocha, M.P., Rodríguez, J.M.C., Fdez-Riverola, F., Valencia, A. (eds) 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Advances in Intelligent and Soft Computing, vol 93. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19914-1_34

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-19914-1_34

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-19913-4

  • Online ISBN: 978-3-642-19914-1

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics