R Code for the data analysis in "Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors" by Chen, et al
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Hybrid_Promoters_Fit.R
Hybridpromoterdata.xlsx
Inducible_Promoters_Fit.R
Inducible_promoters.xlsx
README.md
coordsAra_induced
coordsAra_uninduced
coordsHybrid_Ara_mixed
coordsHybrid_Las_mixed
coordsLas_induced
coordsLas_uninduced
parametersHybrid_Ara_mixed
parametersHybrid_Las_mixed
parameters_Ara
parameters_Las

README.md

Promoter-Engineering

R Code for the data analysis in "Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors" by Chen, et al

The two excel files contain the data that is imported by the two R files.

The inducible promoter data is oragnized according to two main "Conditions": Ara or Las. The third and fourth column in the spreasdsheet determine -35 and -10 condition (in that order), and the fith column gives the measured promoter strength.

There are four conditions for the hybrid promoter data, as explained in more detail in the manuscript and supplementary material. The four conditions are ++, +−, −+, and −− with the first sign denoting inducer absent/present, and the second sign denoting repressed state (ie repressed = -, unrepressed = +). In the spreasheet

1 - is the -/- state in the notes, repressed and no activator 2 - is the +/- state in the notes, repressed with activator 3 - is the -/+ state in the notes, uninduced 4 - is the +/+ state in the notes, activator, but no repression

The R files contain the code that was used to fit the model to the data by minimizing the objective function specified in the Supplentary material.

The remaining files contain the parameters obtained after fitting the data, as well as the predicted "Scores" for the different conditions and models.