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Table 2 Description of the parameter values

From: A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study

Name

Description

Range

Nominal

Units

V IFN

Maximum activation rate of the IFN pathway

[ 2.8,11.2]

6.135

(Molecules/Cell) ∗min

n

Hill coefficient

-

2

Dimensionless

k IFN

Saturation constant for the IFN pathway

[ 0.0022,0.0088]

0.0055

Molecules/Cell

k dIFN

Decay rate of the IFN pathway

[ 0.0232,0.0926]

0.0492

min-1

k I S G F3

Constant for ISGF3 production

[ 0.00012,0.00048]

0.0003

min-1

k d I S G F3

Decay rate of the ISGF3

[ 0.00068,0.00272]

0.0017

min-1

k on

Promoter activation

[ 184.55,738.2]

522.59

min-1

k a I3

Constant of promoter activation by IFN

[ 7681.6,30727]

22687.02

Molecules/Cell

k a I7

Constant of promoter activation by IRF7

[ 13399,53597]

35281.99

Molecules/Cell

k off

Promoter inactivation

[ 0.00044,0.00176]

0.0013

min-1

k Active

IRF7 transcription rate by active promoter

[ 0.5402,2.161]

1.144

min-1

a k Basal

IRF7 basal transcription rate

[ 0.0312,0.125]

0.0861

min-1

b k dmRNA

Decay rate of mRNA

[ 0.029,0.116]

0.0715

min-1

c k I R F7

Translation rate of IRF7

[ 14,56]

43.867

min-1

k d I R F7

Rate of IRF7 phosphorylation

[ 1.540,6.160]

3.877

min-1

k I R F7d i m e r

Rate of IRF7 dimerization

[ 0.235,0.94]

0.602

(Cell/Molecules)/min

k d I R F7d i m e r

Decay rate of IRF7 dimers

[ 0.209,0.836]

0.439

min-1

φ

Scaling factor

-

1

Cell/Molecules

  1. a k Basal was calculated to be at least one order of magnitude smaller than k Active
  2. bDegradation rates for the mRNA were calculated assuming a mRNA half-life in the order of minutes [50]
  3. cBased on the average translation rate in NIH3T3 cells [49]