Skip to main content

Table 2 (Semi-) Quantitative information extracted from literature used for the calibration of the model

From: Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway

Property

Value

Source

1.pRb phosphorylation levels

1.a

  hyper-pRb domination in BCP-ALL cells

qualitative

ALL-specific:

[29]

1.b

  hypo-pRb positive BCP-ALL cells

16 % (±13.2 %)

″

1.c

  hypo-pRb detection threshold

3000 (molecules/cell)

Generic: derived by reference model simulation ([40] and Additional file 2)

2.Cell Kinetics

2.a

  Cycling cells

94 %

ALL-specific:

[29]

2.b

  Quiescent cells

2 %

ALL-specific:

[28, 29]

2.c

  Apoptotic cells

4 %

ALL-specific:

[30]

2.d

  Cycling cells in S/G2/M phases

10 %

ALL-specific:

[25–27]

2.e

  Cycling cells in G1 phase

84 %

ALL-specific:

Derived from 2.a-d (see Additional file 2)

2.f

  Cycling cells in early-G1

13.7 %

ALL-specific:

Derived from 1.b. and 2.a. (see Additional file 2)

3.Cell cycle Timings

3.a

  Mean Cell cycle duration of BCP-ALL cells (T c )

112.5 h (±46.8 h)a

ALL-specific:

[24]

3.b

  S-phase duration in BCP-ALL cells (T s )

18 h

″

3.c

  G2-phase duration

6 h

Generic:

[74]

3.d

  M-phase duration

1 h

″

3.e

  Mean G1-phase duration in BCP-ALL cells

87.5 h (±46.8 h)

Derived from 3.a-d (see Additional file 2)

  Estimated realistic time-range for G1/S transition in BCP-ALL

~2400 - ~8000 min

″

3.f.

  early-G1 phase duration in BCP-ALL cells

~800 min

Derived from 2.f and 3.e (see Additional file 2)

3.g.

  S-phase midpoint

9 h after G1/S transition

ALL-specific (see Additional file 2)

4.Cyclin A levels

4.a

  S-phase passage levels

300 (molecules/cell)

Generic: derived by reference model simulation ([40] and Additional file 2)

4.b

  Levels (rate) before activating modifier activation

<150 (molecules/cell) (<=0 ((molecules/cell)/min))

″

4.c

  Levels after activating modifier activation

<300 (molecules/cell)

″

4.d

  Levels at the midpoint of S-phase

470 (molecules/cell)

″

5.Cyclin D levels

 

  Maximum difference between the initial and the instant levels

500 (molecules/cell)

Generic: derived by reference model simulation [40]

  1. aMean (±standard deviation)