title: Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules.
abstract: We aimed to test the proposal that progressive combinations of multiple promoter elements acting in concert may be responsible for the full range of phases observed in plant circadian output genes. In order to allow reliable selection of informative phase groupings of genes for our purpose, intrinsic cyclic patterns of expression were identified using a novel, non-biased method for the identification of circadian genes. Our non-biased approach identified two dominant, inherent orthogonal circadian trends underlying publicly available microarray data from plants maintained under constant conditions. Furthermore, these trends were highly conserved across several plant species. Four phase-specific modules of circadian genes were generated by projection onto these trends and, in order to identify potential combinatorial promoter elements that might classify genes into these groups, we used a Random Forest pipeline which merged data from multiple decision trees to look for the presence of element combinations. We identified a number of regulatory motifs which aggregated into coherent clusters capable of predicting the inclusion of genes within each phase module with very high fidelity and these motif combinations changed in a consistent, progressive manner from one phase module group to the next, providing strong support for our hypothesis.
authors.affiliation: School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham TW20 0EX, UK.
authors.forename: Sandra P
authors.initials: SP
authors.lastname: Smieszek
authors.affiliation: Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham TW20 0EX, UK Department of Computer Science, Royal Holloway University of London, Egham TW20 0EX, UK.
authors.forename: Haixuan
authors.initials: H
authors.lastname: Yang
authors.affiliation: Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham TW20 0EX, UK Department of Computer Science, Royal Holloway University of London, Egham TW20 0EX, UK.
authors.forename: Alberto
authors.initials: A
authors.lastname: Paccanaro
authors.affiliation: School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham TW20 0EX, UK paul.devlin@rhul.ac.uk.
authors.forename: Paul F
authors.initials: PF
authors.lastname: Devlin
mesh_terms: D057906:Circadian Clocks / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D053263:Gene Regulatory Networks / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D018521:Plant Physiological Phenomena; D011401:Promoter Regions, Genetic / Q000235:genetics*
keywords: Random Forest; clock; dimensionality reduction; microarray; phase