Description: https://doi.org/10.1016%2Fj.cub.2010.12.021
SEEK ID: https://fairdomhub.org/data_files/7449
- Absolute units for proteins in Arabidopsis clock models up to U2020.5
- Predicting absolute levels of clock proteins with a simple model
- Reproducibility documentation
- Construction of NanoLUC-tagged plants
- Recalibrating the clock models for absolute protein levels, to create models U2019.5 and U2020.5
- Estimating DNA-binding affinities for Arabidopsis proteins
- promoter binding affinity calculations on the genome based on PBMs and EMA for CCA1 and LUX
- LUX ensemble of matrices
- CCA1 ensemble of matrices
- CCA1 PBM E-score data Franco-Zorrilla et al
- LUX E-scores data from Helfer et al
- CCA1 peaks from Kamioka et al
- LUX peaks Ezer et al
- LUX genomic regulation using PBMs and EMA
- CCA1 genomic regulation using PBMs and EMA
- CCA1 matrix inference with EMA and PBMs
- LUX matrix inference with EMA and PBMs
- promoter binding affinity calculations on the genome based on PBMs and EMA for CCA1 and LUX
- Measuring absolute levels of clock proteins with calibrated NanoLUC assays
- Testing the inferred transcription rates of a dynamic, gene network model in absolute units (in silico Plants 2021)
- Expanding the bioluminescent reporter toolkit for plant science with NanoLUC
- Abundant clock proteins point to missing molecular regulation in the plant circadian clock
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Created: 25th Aug 2024 at 14:35
Last updated: 19th Dec 2024 at 11:28
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Version 1 (earliest) Created 25th Aug 2024 at 14:35 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/0000-0002-7975-5013SynthSys 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
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 ...
Submitter: Andrew Millar
Studies: Construction of NanoLUC-tagged plants, Estimating DNA-binding affinities for Arabidopsis proteins, Measuring absolute levels of clock proteins with calibrated NanoLUC assays, Predicting absolute levels of clock proteins with a simple model, Recalibrating the clock models for absolute protein levels, to create mo..., Reproducibility documentation
Assays: Clock protein number determination with NanoLUC calibration, Clock proteins NanoLUC fusion raw data, Gatway maps of genomic regions of clock genes, In vivo bioluminescence of clock protein-NanoLUC fusions: example experi..., Jupyter notebook Predicting Protein Numbers, Propagating scaling factors into model parameters for U2019.4->U2019.5 a..., Protein level time series, Python packages, Reproducibility tool set, Selection of complemented transgenic lines, TiMet RNA timeseries data, promoter binding affinity calculations on the genome based on PBMs and E...
Snapshots: Snapshot 1
Submitter: Andrew Millar
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: promoter binding affinity calculations on the genome based on PBMs and E...
Snapshots: No snapshots
The promoter regions for clock genes that present a ChIP-seq signal were extracted from TAIR10 using costume python scripts using the gene list for Kamioka et al CCA1 or Daphne Ezer et al for LUX. The promoter was considered from the TSS of the gene until the annotated end of the upstream gene. Then, this region was scanned using the Energy Matrix derived using EMA working as a classifier for bound or unbound. After classification the calibrated PBM data calibrated using in vitro data was used ...
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units for proteins in Arabidopsis cloc...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: CCA1 PBM E-score data Franco-Zorrilla et al, CCA1 ensemble of matrices, CCA1 peaks from Kamioka et al, LUX E-scores data from Helfer et al, LUX ensemble of matrices, LUX peaks Ezer et al
Snapshots: No snapshots