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Open Access Highly Accessed Methodology article

Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data

Narsis A Kiani* and Lars Kaderali

Author Affiliations

Technische Universität Dresden, Medical Faculty Carl Gustav Carus, Institute for Medical Informatics and Biometry, Fetscherstr. 74, 01307 Dresden, Germany

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BMC Bioinformatics 2014, 15:250  doi:10.1186/1471-2105-15-250

Published: 22 July 2014

Abstract

Background

Network inference deals with the reconstruction of molecular networks from experimental data. Given N molecular species, the challenge is to find the underlying network. Due to data limitations, this typically is an ill-posed problem, and requires the integration of prior biological knowledge or strong regularization. We here focus on the situation when time-resolved measurements of a system’s response after systematic perturbations are available.

Results

We present a novel method to infer signaling networks from time-course perturbation data. We utilize dynamic Bayesian networks with probabilistic Boolean threshold functions to describe protein activation. The model posterior distribution is analyzed using evolutionary MCMC sampling and subsequent clustering, resulting in probability distributions over alternative networks. We evaluate our method on simulated data, and study its performance with respect to data set size and levels of noise. We then use our method to study EGF-mediated signaling in the ERBB pathway.

Conclusions

Dynamic Probabilistic Threshold Networks is a new method to infer signaling networks from time-series perturbation data. It exploits the dynamic response of a system after external perturbation for network reconstruction. On simulated data, we show that the approach outperforms current state of the art methods. On the ERBB data, our approach recovers a significant fraction of the known interactions, and predicts novel mechanisms in the ERBB pathway.