Table 3.
Attractor states of long-term perturbation simulations
| |
BT474 |
HCC1954 |
SKBR3 |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Simulation |
RPS6 |
RB |
RPS6 |
RB |
RPS6 |
RB |
||||||
| A | E | A | E | A | E | A | E | A | E | A | E | |
| X |
1 |
0 |
1 |
1 |
0 |
1 |
1 |
0 |
1 |
|||
| E |
0 |
1 |
0 |
0 |
1 |
0 |
0 |
1 |
0 |
|||
| P |
0 |
- |
0 |
- |
0 |
- |
0 |
- |
0 |
- |
0 |
- |
| T |
1 |
- |
0 |
- |
1 |
- |
0 |
- |
1 |
- |
0 |
- |
| E, P |
0 |
1 |
0 |
0 |
1 |
0 |
0 |
1 |
0 |
|||
| E, T |
0 |
1 |
0 |
0 |
1 |
0 |
0 |
0 |
||||
| P, T |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
||||
| E, P, T | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | |||
The therapeutics erlotinib, trastuzumab and pertuzumab, abbreviated by first letters, that were permanently active in the simulated perturbation conditions besides the stimulus S, standing for the full growth medium, are stored in the column Simulation. No simulated drug treatment is denoted by ‘X’. The A columns hold the attractor states of the proteins RPS6 and RB associated with the perturbations. The E columns contain the protein activity status, statistically deduced from the experimental data. In case of a significant (p-value < 0.05) combined influence of both, drug treatment and time, on the protein signal intensity, a Wilcoxon rank sum test was conducted for the measurements at time point 30 hours. The drug treatments leading to significantly (p-value < 0.05) smaller intensity values compared to the control measurement ‘X’ were considered as efficient inhibitors, resulting in a table entry of zero. Lacking comparable experiments is labelled as ‘-’, while consistency between simulations and experimental observations is printed in bold.