Table 1 List of ODE model parameters, their descriptions, and values
From: Network-dosage compensation topologies as recurrent network motifs in natural gene networks
Parameter | Description | Value |
|---|---|---|
Sa | Activator scale of action | Logarithmically sampled from [10−3, 103] |
Si | Inhibitor scale of action | Logarithmically sampled from [10−4, 102] |
α | Stoichiometry parameter | Linearly sampled from [0.2, 5] |
β | Stoichiometry parameter | Linearly sampled from [0.2, 5] |
θa | Activator production rate | 300, 1500 or 7500/hr |
θi | Inhibitor production rate | 300, 1500 or 7500/hr |
γ0 | Dilution rate constant | 0.46/hr |
ta | Activator half-life | 5, 30, 120 or ∞ min |
γa | Activator degradation rate constant | ln(2)/ta |
ti | Inhibitor half-life | 5, 30, 120 or ∞ min |
γi | Inhibitor degradation rate constant | ln(2)/ti |
N | Network copy number | 1 or 2 |
λa | Activator basal production coefficient | 0.20 |
λi | Inhibitor basal production coefficient | 0.20 |
g | Inducer strength | 10-2+0.025C, where C = 0, 1, 2, …, 80 |