Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum.

Kuang Lin, Dirk Husmeier, Frank Dondelinger, Claus D. Mayer, Hui Liu, Leighton Pritchard, George P. C. Salmond, Ian K. Toth, Paul R. J. Birch

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

    3 Citations (Scopus)

    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.
    Original languageEnglish
    Title of host publicationComputational biology
    EditorsDavid Fenyo
    Place of PublicationNew York
    PublisherHumana Press
    Pages253-281
    Number of pages29
    ISBN (Electronic)9781607618423
    ISBN (Print)9781607618416
    DOIs
    Publication statusPublished - 2010

    Publication series

    NameMethods in Molecular Biology
    Volume673
    ISSN (Print)1064-3745
    ISSN (Electronic)1940-6029

    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

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  • Cite this

    Lin, K., Husmeier, D., Dondelinger, F., Mayer, C. D., Liu, H., Pritchard, L., Salmond, G. P. C., Toth, I. K., & Birch, P. R. J. (2010). Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum. In D. Fenyo (Ed.), Computational biology (pp. 253-281). (Methods in Molecular Biology; Vol. 673). Humana Press. https://doi.org/10.1007/978-1-60761-842-3_17