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Table 2 Systems biology model parameters description and their statistical distributions

From: Systems biology modeling of omics data: effect of cyclosporine a on the Nrf2 pathway in human renal cells

Parameter

Description

Units

Prior distribution

Posterior mode, mean ± SD

v ma x 7

Maximum rate of CsA metabolism

sec−1

LN (0.2, 3)

0.187

0.274 ± 0.233

k f 75

Basal rate of ROS formation

zmol.sec−1

LN (12, 3)

79.1

135 ± 80.8

v ma x 8 b

Maximum rate of ROS metabolism

sec−1

LN (8, 3)

2.67

3.88 ± 2.54

k o x 10

Keap1 oxidation rate constant

zmol−1.sec−1

Uniform (10−8, 10−2)

3.02 × 10−6

3.86 × 10−6 ± 2.72 × 10−6

k ROS

ROS formation rate constant

sec−1

Uniform (10−8, 10−2)

6.55 × 10−5

8.86 × 10−6 ± 3.86 × 10−5

k b 18

Nrf2 and Maf binding rate constant

sec−1

LN (0.003, 3)

0.0124

0.0193 ± 0.0167

k TS P 21

mRNACYP transcription rate constant

sec−1

LN (1.07, 3)

1.29

1.65 ± 1.85

k TS P 28

mRNANrf2 transcription rate constant

sec−1

LN (0.00611, 3)

0.087

0.062 ± 0.0603

k TS P 34

mRNAGS transcription rate constant

sec−1

LN (1.15, 3)

1.07

1.34 ± 0.53

k TS P 42

mRNAGCLC transcription rate constant

sec−1

LN (1.98, 3)

1.28

2.27 ± 1.91

k TS P 48

mRNAGCLM transcription rateconstant

sec−1

LN (3.22, 3)

3.95

4.84 ± 3.79

k TS P 57

mRNAGST transcription rate constant

sec−1

LN (0.242, 3)

0.021

0.553 ± 0.949

k TS P 57 b

mRNAGPx transcription rate constant

sec−1

LN (0.242, 3)

0.098

0.123 ± 0.0779

k TS P 66

mRNAMRP transcription rate constant

sec−1

LN (0.9, 3)

1.22

2.23 ± 3.55

k b 52

GCLC and GCLM binding rate constant

sec−1

LN (2 × 10−5, 3)

4.33 × 10−6

1.09 × 10−5 ± 9.19 × 10−6

k ind NMA 27

Induction coefficient for Nrf2 gene

zmol−1.sec−1

LN (100, 3)

150

236 ± 433

k ind NMA 33

Induction coefficient for GS gene

zmol−1.sec−1

LN (5.95, 3)

2.17

3.85 ± 2.33

k ind NMA 41

Induction coefficient for GCLC gene

zmol−1.sec−1

LN (8.7, 3)

22.1

43.2 ± 25

k ind NMA 47

Induction coefficient for GCLM gene

zmol−1.sec−1

LN (1.6, 3)

3.28

5.75 ± 3.15

k ind NMA 56

Induction coefficient for GST gene

zmol−1.sec−1

LN (11.9, 3)

8.46

10.4 ± 8.61

k ind NMA 56 b

Induction coefficient for GPx gene

zmol−1.sec−1

LN (11.9, 3)

1.37

6.75 ± 6.51

k ind NMA 65

Induction coefficient for MRP gene

zmol−1.sec−1

LN (16, 3)

6.43

9.62 ± 7.85

v max GCL 72

Maximum rate of γ-GC synthesis by GCL

sec−1

LN (8.2, 3)

83.4

80.3 ± 67.5

v max GCLC 72

Maximum rate of γ-GC synthesis by GCLC

sec−1

LN (1.9, 3)

1.64

2.16 ± 3.11

v ma x 73

Maximum rate of GSH synthesis

sec−1

LN (6.5, 3)

8.57

10.3 ± 4.43

v ma x 74

Maximum rate of GSH degradation

zmol.sec−1

LN (1845, 3)

283

374 ± 353

Km 74

Michaelis-Menten constant of GSH degradation

zmol

LN (2 × 107, 3)

1.62 × 108

2.22 × 108 ± 2.36 × 108

  1. *: 1 zmol = 1 zeptomole = 10−21 mol.
  2. **: LN: Log-normal distribution (mean, SD).