Projects: COSMIC
Institutions: University of Ulm
Phd student University of Ulm Institute of Microbiology and Biotechnology Albert-Einstein- Allee 11 89069 Ulm, Germany
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...
Assay: _A_05_BUSCO Short Name: 05_BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO post filtering and reassignment Description: BUSCO post filtering and reassignment pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: _A_02.3_InterProScan Short Name: 02.3_InterProScan Assay Class: DRY Assay Type: InterProScan Title: InterProScan on tr2aacds output Description: InterProScan on tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Creators: None
Submitter: Lorenzo Tagliazucchi
Creators: None
Submitter: Lorenzo Tagliazucchi
Creator: Joerg Stuelke
Submitter: Leif Steil
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List of protein identified proteins in SPINE experiment.
Creators: Joerg Stuelke, Uwe Voelker
Submitter: Leif Steil
The phosphorylation level of a particular protein can be determined using a procedure based upon western immunoblotting, with Phos-tag™ reagent present in the SDS-PAGE gel. The Phos-tag™ reagent, supplied in the form of Phos-tag™ acrylamide (Wako Pure Chemical Industries, AAL-107), causes proteins to be resolved both on the basis of size and phosphorylation state. This means that phosphorylated and de-phosphorylated forms of the same protein can be distinguished.
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
