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
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
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)
Center for the Study of Biological Complexity, http://www.vcu.edu/csbc/
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)
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
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)
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)
Malutan, R., Gómez, P., Borda, M.: Independent component analysis algorithms for microarray data analysis. Intelligent Data Analysis Journal 14(2), 193–206 (2010)
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)
Zhang, L., Miles, M.F., Aldape, K.D.: A model of molecular interactions on short oligonucleotide microarrays. Nature Biotechnology 21(7), 818–821 (2003)
Zhang, Y., Hammer, D.A., Graves, D.J.: Competitive Hybridization Kinetics Reveals Unexpected Behavior Patterns. Biophysical Journal 89, 2950–2959 (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights 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)