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The use of semiparametric mixed models to analyze PamChip® peptide array data: an application to an oncology experiment

(2011) BIOINFORMATICS. 27(20). p.2859-2865
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Abstract
Motivation: Phosphorylation by protein kinases is a central theme in biological systems. Aberrant protein kinase activity has been implicated in a variety of human diseases (e.g. cancer). Therefore, modulation of kinase activity represents an attractive therapeutic approach for the treatment of human illnesses. Thus, identification of signature peptides is crucial for protein kinase targeting and can be achieved by using PamChip (R) microarray technology. We propose a flexible semiparametric mixed model for analyzing PamChip (R) data. This approach enables the estimation of the phosphorylation rate (Velocity) as a function of time together with pointwise confidence intervals. Results: Using a publicly available dataset, we show that our model is capable of adequately fitting the kinase activity profiles and provides velocity estimates over time. Moreover, it allows to test for differences in the velocity of kinase inhibition between responding and non-responding cell lines. This can be done at individual time point as well as for the entire velocity profile.

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MLA
Thilakarathne, Pushpike J, Lieven Clement, Dan Lin, et al. “The Use of Semiparametric Mixed Models to Analyze PamChip® Peptide Array Data: An Application to an Oncology Experiment.” BIOINFORMATICS 27.20 (2011): 2859–2865. Print.
APA
Thilakarathne, Pushpike J, Clement, L., Lin, D., Shkedy, Z., Kasim, A., Talloen, W., Versele, M., et al. (2011). The use of semiparametric mixed models to analyze PamChip® peptide array data: an application to an oncology experiment. BIOINFORMATICS, 27(20), 2859–2865.
Chicago author-date
Thilakarathne, Pushpike J, Lieven Clement, Dan Lin, Ziv Shkedy, Adetayo Kasim, Willem Talloen, Matthias Versele, and Geert Verbeke. 2011. “The Use of Semiparametric Mixed Models to Analyze PamChip® Peptide Array Data: An Application to an Oncology Experiment.” Bioinformatics 27 (20): 2859–2865.
Chicago author-date (all authors)
Thilakarathne, Pushpike J, Lieven Clement, Dan Lin, Ziv Shkedy, Adetayo Kasim, Willem Talloen, Matthias Versele, and Geert Verbeke. 2011. “The Use of Semiparametric Mixed Models to Analyze PamChip® Peptide Array Data: An Application to an Oncology Experiment.” Bioinformatics 27 (20): 2859–2865.
Vancouver
1.
Thilakarathne PJ, Clement L, Lin D, Shkedy Z, Kasim A, Talloen W, et al. The use of semiparametric mixed models to analyze PamChip® peptide array data: an application to an oncology experiment. BIOINFORMATICS. 2011;27(20):2859–65.
IEEE
[1]
P. J. Thilakarathne et al., “The use of semiparametric mixed models to analyze PamChip® peptide array data: an application to an oncology experiment,” BIOINFORMATICS, vol. 27, no. 20, pp. 2859–2865, 2011.
@article{3003060,
  abstract     = {Motivation: Phosphorylation by protein kinases is a central theme in biological systems. Aberrant protein kinase activity has been implicated in a variety of human diseases (e.g. cancer). Therefore, modulation of kinase activity represents an attractive therapeutic approach for the treatment of human illnesses. Thus, identification of signature peptides is crucial for protein kinase targeting and can be achieved by using PamChip (R) microarray technology. We propose a flexible semiparametric mixed model for analyzing PamChip (R) data. This approach enables the estimation of the phosphorylation rate (Velocity) as a function of time together with pointwise confidence intervals. 
Results: Using a publicly available dataset, we show that our model is capable of adequately fitting the kinase activity profiles and provides velocity estimates over time. Moreover, it allows to test for differences in the velocity of kinase inhibition between responding and non-responding cell lines. This can be done at individual time point as well as for the entire velocity profile.},
  author       = {Thilakarathne, Pushpike J and Clement, Lieven and Lin, Dan and Shkedy, Ziv and Kasim, Adetayo and Talloen, Willem and Versele, Matthias and Verbeke, Geert},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  language     = {eng},
  number       = {20},
  pages        = {2859--2865},
  title        = {The use of semiparametric mixed models to analyze PamChip® peptide array data: an application to an oncology experiment},
  url          = {http://dx.doi.org/10.1093/bioinformatics/btr475},
  volume       = {27},
  year         = {2011},
}

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