Linking U2019.5 and U2020.5 to protein data in absolute number of molecules per cell and in vivo Version 1
This describes how models were linked to in vitro data and then from there also linked to in-vivo data by detrending and rescaling in vivo data to match in vitro data for CCA1 and TOC1. The detrending was also derived by performing a long LD experiemnt fro servarl days and using the expression peaks of TOC1 to extract the trend in NLUC decay and plant growth.
SEEK ID: https://fairdomhub.org/documents/4303?version=1
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Linking_U2019_5_and_U2020_5_to_NLdata_and_vivo.ipynb
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Created: 27th Aug 2024 at 08:26
Last updated: 19th Dec 2024 at 11:29
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Version 1 (earliest) Created 27th Aug 2024 at 08:26 by Uriel Urquiza Garcia
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Projects: Millar group, PlaSMo model repository, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, Light and plant development, Light control of leaf development, Toggle switch, Reduce Complexity (RCO) reconstruction, Model Driven Prime Editing, PULSE 2.0, Plant optogenetics
Institutions: University of Edinburgh, Heinrich Heine University of Düsseldorf
https://orcid.org/0000-0002-7975-5013
SynthSys 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
The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025.
Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted using a simple model from the TiMet ...
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