International Journal of applied mathematics and computer science

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Paper details

Number 3 - September 2003
Volume 13 - 2003

Properties of a singular value decomposition based dynamical model of gene expression data

Krzysztof Simek

Recently, data on multiple gene expression at sequential time points were analyzed using the Singular Value Decomposition (SVD) as a means to capture dominant trends, called characteristic modes, followed by the fitting of a linear discrete-time dynamical system in which the expression values at a given time point are linear combinations of the values at a previous time point. We attempt to address several aspects of the method. To obtain the model, we formulate a nonlinear optimization problem and present how to solve it numerically using the standardMATLAB procedures. We use freely available data to test the approach. We discuss the possible consequences of data regularization, called sometimes “polishing”, on the outcome of the analysis, especially when the model is to be used for prediction purposes. Then, we investigate the sensitivity of the method to missing measurements and its abilities to reconstruct the missing data. Summarizing, we point out that approximation of multiple gene expression data preceded by SVD provides some insight into the dynamics, but may also lead to unexpected difficulties, like overfitting problems.

multiple gene expression, singular value decomposition, dynamical model of gene expression data