Format

Send to

Choose Destination
See comment in PubMed Commons below
J R Soc Interface. 2014 Oct 6;11(99). pii: 20140535. doi: 10.1098/rsif.2014.0535.

Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules.

Author information

1
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.
2
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.
3
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.

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.

KEYWORDS:

Random Forest; clock; dimensionality reduction; microarray; phase

PMID:
25142519
PMCID:
PMC4233729
DOI:
10.1098/rsif.2014.0535
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Support Center