Inference of circadian regulatory networks

Grzegorczyk, M., Aderhold, A., Smith, V. A. and Husmeier, D. (2014) Inference of circadian regulatory networks. In: Ortuno, F. and Rojas, I. (eds.) International Work-Conference on Bioinformatics and Biomedical Engineering. Copicentro Granada S.L: Granada, pp. 1001-1014. ISBN 9788415814849

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Abstract

We assess the accuracy of various state-of-the-art methods for reconstructing gene and protein regulatory networks in the context of circadian regulation. Gene expression and protein concentration time series are simulated from a recently published regulatory network of the circadian clock in A. thaliana, which is mathematically described by a Markov jump process based on Michaelis-Menten kinetics. Our study provides relative network reconstruction accuracy scores for a critical comparative performance evaluation, quantifies the influence of systematically missing values related to unknown protein concentrations and mRNA transcription rates, and investigates the dependence of the performance on the network topology and the degree of recurrency. An application to recent gene expression time series from qPCR experiments suggests new hypotheses about the structure of the central circadian gene regulatory network in A. thaliana.

Item Type:Book Sections (Other)
Status:Published
Glasgow Author(s) Enlighten ID:Aderhold, Mr Andrej and Husmeier, Professor Dirk
Authors: Grzegorczyk, M., Aderhold, A., Smith, V. A., and Husmeier, D.
College/School:College of Science and Engineering > School of Mathematics and Statistics > Statistics
Publisher:Copicentro Granada S.L
ISBN:9788415814849

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