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Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks

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Penfold, Christopher A., Buchanan-Wollaston, Vicky, Denby, Katherine J. and Wild, David L.. (2012) Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks. Bioinformatics, Vol.28 (No.12). i233-i241. ISSN 1367-4803

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Abstract

Motivation: The generation of time series transcriptomic datasets collected under multiple experimental conditions has proven to be a powerful approach for disentangling complex biological processes, allowing for the reverse engineering of gene regulatory networks (GRNs). Most methods for reverse engineering GRNs from multiple datasets assume that each of the time series were generated from networks with identical topology. In this study, we outline a hierarchical, non-parametric Bayesian approach for reverse engineering GRNs using multiple time series that can be applied in a number of novel situations including: (i) where different, but overlapping sets of transcription factors are expected to bind in the different experimental conditions; that is, where switching events could potentially arise under the different treatments and (ii) for inference in evolutionary related species in which orthologous GRNs exist. More generally, the method can be used to identify context-specific regulation by leveraging time series gene expression data alongside methods that can identify putative lists of transcription factors or transcription factor targets.

Results: The hierarchical inference outperforms related (but non-hierarchical) approaches when the networks used to generate the data were identical, and performs comparably even when the networks used to generate data were independent. The method was subsequently used alongside yeast one hybrid and microarray time series data to infer potential transcriptional switches in Arabidopsis thaliana response to stress. The results confirm previous biological studies and allow for additional insights into gene regulation under various abiotic stresses.

Availability: The methods outlined in this article have been implemented in Matlab and are available on request.

Item Type: Journal Article
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH301 Biology
Divisions: Faculty of Science > Life Sciences (2010- )
Faculty of Science > Centre for Systems Biology
Library of Congress Subject Headings (LCSH): Genetic regulation -- Statistical methods, Time-series analysis, Bayesian statistical decision theory
Journal or Publication Title: Bioinformatics
Publisher: Oxford University Press
ISSN: 1367-4803
Official Date: 2012
Volume: Vol.28
Number: No.12
Page Range: i233-i241
Identification Number: 10.1093/bioinformatics/bts222
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
Funder: Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Engineering and Physical Sciences Research Council (EPSRC)
Grant number: BB/F005806/1 (BBSRC), EP/I036575/1 (EPSRC)
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URI: http://wrap.warwick.ac.uk/id/eprint/48097

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