title: An integrated network of Arabidopsis growth regulators and its use for gene prioritization.
abstract: Elucidating the molecular mechanisms that govern plant growth has been an important topic in plant research, and current advances in large-scale data generation call for computational tools that efficiently combine these different data sources to generate novel hypotheses. In this work, we present a novel, integrated network that combines multiple large-scale data sources to characterize growth regulatory genes in Arabidopsis, one of the main plant model organisms. The contributions of this work are twofold: first, we characterized a set of carefully selected growth regulators with respect to their connectivity patterns in the integrated network, and, subsequently, we explored to which extent these connectivity patterns can be used to suggest new growth regulators. Using a large-scale comparative study, we designed new supervised machine learning methods to prioritize growth regulators. Our results show that these methods significantly improve current state-of-the-art prioritization techniques, and are able to suggest meaningful new growth regulators. In addition, the integrated network is made available to the scientific community, providing a rich data source that will be useful for many biological processes, not necessarily restricted to plant growth.
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Ehsan
authors.initials: E
authors.lastname: Sabaghian
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Zuzanna
authors.initials: Z
authors.lastname: Drebert
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Inzé
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.|Inflammation Research Center, VIB, 9052 Gent, Belgium.|Department of Respiratory Medicine, Ghent University Hospital, Gent, Belgium.
authors.forename: Yvan
authors.initials: Y
authors.lastname: Saeys
mesh_terms: D017360:Arabidopsis / Q000502:physiology*; D053263:Gene Regulatory Networks / Q000502:physiology*; D017343:Genes, Plant / Q000502:physiology*; D010937:Plant Growth Regulators / Q000235:genetics / Q000378:metabolism*
chemical_list: D010937:Plant Growth Regulators