Reconstruction of mammalian cell cycle regulatory network from microarray data using stochastic logical networks

Authors:
Bartek Wilczyński;Jerzy Tiuryn
Affiliations:
Institute of Mathematics, Polish Academy of Sciences, Warsaw, Poland;Institute of Informatics, Warsaw University, Warsaw, Poland
Venue:
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Year:
2007

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Abstract

We present a novel algorithm for reconstructing the topology of regulatory networks based on the Stochastic Logical Network model. Our method, by avoiding the computation of the Markov model parameters is able to reconstruct the topology of the SLN model in polynomial time instead of exponential as in previous study [29]. To test the performance of the method, we apply it to different datasets (both synthetic and experimental) covering the expression of several cell cycle regulators which have been thoroughly studied [18,11]. We compare the results of our method with the popular Dynamic Bayesian Network approach in order to quantify the ability to reconstruct true dependencies. Although both methods able to recover only a part of the true dependencies from realistic data, our method gives consistently better results than Dynamic Bayesian Networks in terms of the number of correctly reconstructed edges, sensitivity and statistical significance.