Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum.
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.
Lin
Kuang
K
Biomathematics and Statistics Scotland, Edinburgh & Aberdeen, UK.
Husmeier
Dirk
D
Dondelinger
Frank
F
Mayer
Claus D
CD
Liu
Hui
H
Prichard
Leighton
L
Salmond
George P C
GP
Toth
Ian K
IK
Birch
Paul R J
PR
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