Data analysis and modelling scripts and results for the Seaton et al. 2017 study, from Daniel Seaton.
SEEK ID: https://fairdomhub.org/studies/303
Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Projects: Millar group, TiMet
Study position:
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Created: 16th Nov 2017 at 12:22
Last updated: 20th Feb 2018 at 22:03
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Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Institutions: University of Edinburgh
https://orcid.org/0000-0003-1756-3654SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Web page: http://www.synthsys.ed.ac.uk
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri
EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015. "TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."
Programme: SynthSys
Public web page: http://timing-metabolism.eu/
Organisms: Arabidopsis thaliana, Ostreococcus tauri
Click on Snapshot 2 to download data, models and analysis for Daniel Seaton et al. biorXiv 2017 https://doi.org/10.1101/182071 and Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962. Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.
Submitter: Andrew Millar
Studies: Modelling and analysis of translational coincidence, Photoperiod-specific proteome data for Arabidopsis, Proteome and translation rate data for the Ostreococcus alga and for cya..., Rhythmic and photoperiod-specific transcriptome datasets for Arabidopsis
Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Blasing et al, 2005, diurnal microarray in 12L:12D, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data, Photoperiod proteomics, Stitt lab, TiMet photoperiod microarrays, Translational coincidence model
Snapshots: Snapshot 1, Snapshot 2
These Python scripts define and simulate the translational coincidence model. This model takes measured transcript dynamics (Blasing et al, 2005) in 12L:12D, measured synthesis rates of protein in light compared to dark (Pal et al, 2013), and outputs predicted changes in protein abundance between short (6h) and long (18h) photoperiods. These are compared to the photoperiod proteomics dataset we generated.
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Photoperiodic control of the Arabidopsis proteo...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: Translational coincidence modelling - python sc...
SOPs: No SOPs
Data files: Blasing et al, 2005, diurnal microarray dataset..., Table EV1 - Quantitative proteomics dataset
Snapshots: No snapshots
Mean and standard deviation of protein abundances in 6h, 8h, 12h, and 18h photoperiods.
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Creator: Daniel Seaton
Submitter: Daniel Seaton
Creator: Daniel Seaton
Submitter: Daniel Seaton
Model type: Algebraic equations
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Photoperiodic control of the Arabidopsis proteo...
Studies: Modelling and analysis of translational coincid...
Assays: Translational coincidence model