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. Author manuscript; available in PMC: 2021 Apr 22.
Published in final edited form as: Cell Syst. 2020 Apr 22;10(4):363–378.e12. doi: 10.1016/j.cels.2020.03.004
parameters sampling range
independent model parameters
ron The rate at which DNA is activated. 0.001 - 0.1
roff The rate at which DNA is inactivated. 0.01 - 0.1
rprod Synthesis rate of gene product. 0.01 - 1
rdeg Degradation rate of gene product. 0.001 - 0.1
radd Parameter determining the contribution of the additional DNA activation rate upon gene regulation. 0.1 - 1
d Factor by which the mRNA synthesis rate is increased when in an active DNA state. d >1. 2 - 100
n Hill coefficient. 0.1 - 10
dependent model parameters
k* Dissociation constant of the Hill function, where k(rprod,rdeg,d)=0.95drprodrdeg -
dependent classification parameters
thres** Threshold above which a gene is thought of being highly expressed, where
thres=0.8drprodrdeg
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