Table 2.
Comparison of simulation results with experimental data (p-pRB protein data and 7-AAD DNA data).
| Simulated | p-pRB data | 7-AAD data | Improved rules | |
| MOCK | 1 | 1 | 1 | 1 |
| AKT1 | 1 | 1 | 1 | 1 |
| MEK1 | 1 | 1 | 1 | 1 |
| CDK2 | 1 | 1 | 1 | 1 |
| CDK4 | 0 | 0 | 0 | 0 |
| p21 | 1 | 1 | 1 | 1 |
| p27 | 1 | 1 | 1 | 1 |
| Cyclin D1 | 0 | 0 | 0 | 0 |
| ERBB2_3 | 1 | 1 | 1 | 1 |
| ERBB1_3 | 0/1 | 1 | 1 | 0/1 |
| ERBB1 | 1 | 0 | 1 | 1 |
| ERBB1_2 | 0/1 | 0 | 1 | 0/1 |
| IGF1R | 1 | 0 | 1 | 1 |
| CDK6 | 0 | 0 | 1 | 0 |
| ER-α | 1 | 0 | 0 | 0 |
| c-MYC | 1 | 0 | 0 | 0 |
| Cyclin E1 | 1 | 0 | 0 | 1 |
The first column ("Simulated") corresponds to the results of knockdown simulations for the initial logical model, while the last column ("Improved rules") displays the results obtained with the revised model (improved logical rules for Cyclin D1 as shown in Table 1). In the "Simulated", "p-pRB data" and "Improved rules" columns, the value "1" denotes the phosphorylation of pRB (G1/S transition) and "0" denotes the lack of phosphorylation (no G1/S transition). In the "7-AAD data" column, the value "1" denotes a low ratio of G1/S (G1/S transition) and "0" denotes a high G1/S ratio (no G1/S transition). Bold numbers emphasize the knockdowns for which simulations and both experiments agree. Normal numbers correspond to the knockdowns for which experiments led to different values, one of them being met by our simulation results. In the case of ERBB1_3 knockdown, one of the two existing stable states meets the concordant experimental result. The final state depends on the choice of the initial conditions, but these are difficult to fully specify (a similar situation occurs for the ERBB1_2 knockdown). Finally, Italic numbers denote the knockdowns for which simulation data differ from the results of both experiments.