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Open AccessArticle

A Synthetic Kinome Microarray Data Generator

Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada
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Academic Editor: Alexander Nesterov-MÃijller
Microarrays 2015, 4(4), 432-453; https://doi.org/10.3390/microarrays4040432
Received: 9 June 2015 / Revised: 25 August 2015 / Accepted: 10 October 2015 / Published: 16 October 2015
(This article belongs to the Special Issue Peptide Microarrays)
Cellular pathways involve the phosphorylation and dephosphorylation of proteins. Peptide microarrays called kinome arrays facilitate the measurement of the phosphorylation activity of hundreds of proteins in a single experiment. Analyzing the data from kinome microarrays is a multi-step process. Typically, various techniques are possible for a particular step, and it is necessary to compare and evaluate them. Such evaluations require data for which correct analysis results are known. Unfortunately, such kinome data is not readily available in the community. Further, there are no established techniques for creating artificial kinome datasets with known results and with the same characteristics as real kinome datasets. In this paper, a methodology for generating synthetic kinome array data is proposed. The methodology relies on actual intensity measurements from kinome microarray experiments and preserves their subtle characteristics. The utility of the methodology is demonstrated by evaluating methods for eliminating heterogeneous variance in kinome microarray data. Phosphorylation intensities from kinome microarrays often exhibit such heterogeneous variance and its presence can negatively impact downstream statistical techniques that rely on homogeneity of variance. It is shown that using the output from the proposed synthetic data generator, it is possible to critically compare two variance stabilization methods. View Full-Text
Keywords: kinome array; synthetic data; normalization; heteroscedasticity of variance kinome array; synthetic data; normalization; heteroscedasticity of variance
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Maleki, F.; Kusalik, A. A Synthetic Kinome Microarray Data Generator. Microarrays 2015, 4, 432-453.

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