Document details for 'Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum'

Authors Lin, K., Husmeier, D., Dondelinger, F., Mayer, C-D., Liu, H., Pritchard, L., Salmond, G., Toth, I.K. and Birch, P.R.J.
Publication details In "Computational Biology", 253-281. Eds. David Fenyo. Humana Press.
Publisher details Humana Press
Keywords Pectobacterium atrosepticum, quorum sensing, transposon mutagenesis, microarrays, graphical Gaussian models, sparse Bayesian regression, LASSO, Bayesian networks, nested effects models, degree distribution, power law, gene ontologies.
Abstract The objective of the project reported in the present chapter was the reverse engineering of gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum from micorarray gene expression profiles, obtained from the wild type and eight knock-out strains. To this end, we have applied various recent methods from multivariate statistics and machine learning: graphical Gaussian models, sparse Bayesian regression, LASSO (least absolute shrinkage and selection operator), Bayesian networks, and nested effects models. We have investigated the degree of similarity between the predictions obtained with the different approaches, and we have assessed the consistency of the reconstructed networks in terms of global topological network properties, based on the node degree distribution. The chapter concludes with a biological evaluation of the predicted network structures.
ISBN 978-1-60761-841-6.
Last updated 2011-04-08
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    http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-60761-842-3_17

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