title: Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum.
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 knockout 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.
authors.affiliation: Biomathematics and Statistics Scotland, Edinburgh & Aberdeen, UK.
authors.forename: Kuang
authors.initials: K
authors.lastname: Lin
authors.forename: Dirk
authors.initials: D
authors.lastname: Husmeier
authors.forename: Frank
authors.initials: F
authors.lastname: Dondelinger
authors.forename: Claus D
authors.initials: CD
authors.lastname: Mayer
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.forename: Leighton
authors.initials: L
authors.lastname: Prichard
authors.forename: George P C
authors.initials: GP
authors.lastname: Salmond
authors.forename: Ian K
authors.initials: IK
authors.lastname: Toth
authors.forename: Paul R J
authors.initials: PR
authors.lastname: Birch
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D003198:Computer Simulation; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D005818:Genetic Engineering / Q000379:methods*; D008954:Models, Biological; D016011:Normal Distribution; D044043:Pectobacterium / Q000235:genetics*; D010944:Plants / Q000382:microbiology*; D053038:Quorum Sensing / Q000235:genetics*; D012372:ROC Curve; D012044:Regression Analysis; D012984:Software