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Code for joint probabilistic inference of transcription factor behaviour and gene-transcription factor as well as metabolite-transcription factor interaction based on genome and metabolite data.
Bayesian model for inference of the activity of transcription factors from targets' mRNA levels. A standalone C sharp package (runs on linux and mac under MONO).
The zip file contains two executable Matlab functions.
File named 'fnct_gen_tfcompmod.m' generates a Simbiology model based on the following interactions:
R + X <-> RX -> R + X + Px
R + Y <-> RY -> R + Y + Py
R + Z <-> RZ -> R + Z + Pz
Y + Pz -> Pz
We assume much higher reaction speeds of sigma factor RNApol binding/unbinding compared to protein expression. Protein expression can therefore be represented by Michaelis-Menten like kinetic laws with three competing inhibitors