promoter binding affinity calculations on the genome based on PBMs and EMA for CCA1 and LUX
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 for assigning an dissociation constant (Kd). This was performed by inverting Ka=1/Kd and adding up for the full promoter the affinity contribution of each 8-mere. The resulting total Ka was then inverted once more to derive a total dissociation constant, which we report in Supplementary table X. The z-scores for each promoter were calculated by concatenating the genome and sampling randomly regions of the same size of the promoter 1,000. Total dissociation constants for each of the sample regions as was done for their cognate promoter region. The values were ln-transformed and the z-score calculated accordingly with (x-mu)/sigma.
SEEK ID: https://fairdomhub.org/assays/2489
Modelling analysis
Projects: Millar group
Investigation: Absolute units for proteins in Arabidopsis clock models up to U2020.5
Study: Estimating DNA-binding affinities for Arabidopsis proteins
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: No organisms
Export PNG
Download
Creators and Submitter
Views: 18
Created: 25th Aug 2024 at 13:45
Last updated: 19th Dec 2024 at 11:28
TagsThis item has not yet been tagged.
Related items
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 ...
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...
Submitter: Andrew Millar
Investigation: Absolute units for proteins in Arabidopsis cloc...
Assays: promoter binding affinity calculations on the genome based on PBMs and E...
The file contains the matrices that come from the MCMH sampling during the inference process from PBMs
The file contains the matrices that come from the MCMH sampling during the inference process from PBMs
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
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 ...
Creator: Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
