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Title: Stochastic dynamic modeling of short gene expression time-series data
Authors: Wang, Z
Yang, F
Swift, S
Tucker, A
Liu, X
Keywords: Clustering; DNA microarray technology; expectation maximization (EM) algorithm; Gene expression; Modeling;time-series data
Issue Date: 2008
Publisher: IEEE
Description: Copyright [2008] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to By choosing to view this document, you agree to all provisions of the copyright laws protecting it.
In this paper, the expectation maximization (EM) algorithm is applied for modeling the gene regulatory network from gene time-series data. The gene regulatory network is viewed as a stochastic dynamic model, which consists of the noisy gene measurement from microarray and the gene regulation first-order autoregressive (AR) stochastic dynamic process. By using the EM algorithm, both the model parameters and the actual values of the gene expression levels can be identified simultaneously. Moreover, the algorithm can deal with the sparse parameter identification and the noisy data in an efficient way. It is also shown that the EM algorithm can handle the microarray gene expression data with large number of variables but a small number of observations. The gene expression stochastic dynamic models for four real-world gene expression data sets are constructed to demonstrate the advantages of the introduced algorithm. Several indices are proposed to evaluate the models of inferred gene regulatory networks, and the relevant biological properties are discussed.
Other Identifiers: IEEE Transactions on NanoBioscience, 7(1): 44-55
Appears in Collections:College of Engineering, Design and Physical Sciences

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