Zeilinger2006_PRR7-PRR9light-Yprime

  public model
Short description

The model reproduces the time profile of TOC1 and Y mRNA for a 8:16 cycle as depicted in Fig7A and 7B. A simple algorithm in the event section accomplishes the 8 hour light and 16 hour dark cycle. The model was successfully tested on MathSBML


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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Format
SBML (L2V1)
Related Publication
  • A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9.
  • Zeilinger MN, Farré EM, Taylor SR, Kay SA, Doyle FJ 3rd
  • Molecular Systems Biology , 0/ 2006 , Volume 2 , pages: 58
  • Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA.
  • In plants, as in animals, the core mechanism to retain rhythmic gene expression relies on the interaction of multiple feedback loops. In recent years, molecular genetic techniques have revealed a complex network of clock components in Arabidopsis. To gain insight into the dynamics of these interactions, new components need to be integrated into the mathematical model of the plant clock. Our approach accelerates the iterative process of model identification, to incorporate new components, and to systematically test different proposed structural hypotheses. Recent studies indicate that the pseudo-response regulators PRR7 and PRR9 play a key role in the core clock of Arabidopsis. We incorporate PRR7 and PRR9 into an existing model involving the transcription factors TIMING OF CAB (TOC1), LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED (CCA1). We propose candidate models based on experimental hypotheses and identify the computational models with the application of an optimization routine. Validation is accomplished through systematic analysis of various mutant phenotypes. We introduce and apply sensitivity analysis as a novel tool for analyzing and distinguishing the characteristics of proposed architectures, which also allows for further validation of the hypothesized structures.
Contributors
null Molecular Systems Biology

Metadata information

is
BioModels Database MODEL4025650992
BioModels Database BIOMD0000000097
KEGG Pathway ath04710
Gene Ontology GO:0007623
isDerivedFrom
BioModels Database BIOMD0000000055
isDescribedBy
PubMed 17102803
hasTaxon
Curation status
Curated
  • Model originally submitted by : null Molecular Systems Biology
  • Submitted: 13-Mar-2007 22:26:59
  • Last Modified: 05-Jul-2012 15:41:50
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 05-Jul-2012 15:41:50
    • Submitted by: null Molecular Systems Biology
    • With comment: Current version of Zeilinger2006_PRR7-PRR9light-Yprime
  • Version: 1 public model Download this version
    • Submitted on: 13-Mar-2007 22:26:59
    • Submitted by: null Molecular Systems Biology
    • With comment: Original import of PRR7-PRR9light-Yprime
Curator's comment:
(added: 13 Mar 2007, 01:21:45, updated: 13 Mar 2007, 01:21:45)
Shown above are time profiles of TOC1 mRNA and Y mRNA for a 8:16 light/dark cycle as depicted in Fig 7A and 7B of the paper. Simulation results obtained from MathSBML.