Table 1. Validations of model predictions in the in silico knock-out tests.
| Gene deleted | Activated node | Reported effects from literature | References | Predictions | Verified status |
| p53 | DNA damage | Expression level of Fas enhanced | [26] | DNA damage promoted upregulation of FAS | Verified by literature |
| p53 | LATS2 | Cell death enhanced | [27] | LATS2 induced apoptosis | Verified by literature |
| p53 | DNA damage | Expression level of CHEK1 enhanced | [28] | DNA damage promoted upregulation of CHEK1 | Verified by literature |
| P53 | KLF4 | CCNB1 reduced | [29] | KLF4 reduced expression of CCNB1 | Verified by literature |
| P53 | ATM | ATM enhanced CHEK1 | Verified in this publication | ||
| P53 | ATR | ATR enhanced CHEK1 | Verified in this publication | ||
| P53 | MAPK14 | Stimulation of BAX | [59] | BAX enhanced | Consistent with prediction |
| VEGFA | SERPINB5 | Apoptosis enhanced in the presence of MMP3 and MMP9 inhibition | [60] | Apoptosis enhanced | Consistent with prediction |
| MDM2 | ATM | DYRK2 induced in the presence and absence of DNA damage | [61] | DYRK2 enhanced | Consistent with prediction |
| MDM2 | ATR | DYRK2 induced in the presence and absence of DNA damage | [61] | DYRK2 enhanced | Consistent with prediction |
| CDK2 | CDKN1A | Apoptosis decreased but not confirmed directly | [62], [63] | Apoptosis reduced | Consistent with prediction |
| CDK2 | CDKN1A | CDK2 regulates senescence suppression by MYC | [55] | Cellular senescence increased | Consistent with prediction |
| P53 | SGK | Cellular senescence decreased | PNP | ||
| P53 | MAPK14 | Cellular senescence decreased | PNP | ||
| P53 | LATS2 | Cellular senescence decreased | PNP | ||
| VEGFA | FOXM1 | Cellular senescence decreased | PNP | ||
| P53 | IFNA1 | CDK4 reduced | PNP | ||
| P53 | IFNA1 | FGF2 reduced | PNP | ||
| P53 | PPM1D | CHEK1 reduced | PNP | ||
| P53 | SFN | CCNB1 reduced | PNP | ||
| P53 | DNA damage | CDK4 reduced | PNP | ||
| P53 | DNA damage | FGF2 reduced | PNP | ||
| P53 | FGF2 | CDK4 enhanced | PNP | ||
| P53 | FOXM1 | CCNB1 enhanced | PNP | ||
| P53 | FAS | Apoptosis enhanced | PNP | ||
| P53 | PTTG1 | CDK4 enhanced | PNP | ||
| P53 | PTTG1 | FGF2 enhanced | PNP | ||
| P53 | IFNA1 | FAS enhanced | PNP | ||
| P53 | DYRK2 | P53AIP1 enhanced | PNP | ||
| P53 | DYRK2 | Apoptosis enhanced | PNP | ||
| P53 | MAPK14 | MMP2 enhanced | PNP | ||
| P53 | MAPK14 | SGK enhanced | PNP | ||
| MYC | TCF7L2 | Apoptosis reduced | PNP | ||
| VEGFA | TLR3 | CXCR4 reduced | PNP | ||
| VEGFA | TLR3 | TNFRSF10B reduced | PNP | ||
| VEGFA | CXCR4 | TNFRSF10B enhanced | PNP | ||
| VEGFA | CXCR4 | Apoptosis enhanced | PNP | ||
| VEGFA | FOXM1 | MMP2 enhanced | PNP | ||
| VEGFA | FOXM1 | BAX enhanced | PNP | ||
| VEGFA | FOXM1 | CCNB1 enhanced | PNP | ||
| VEGFA | FOXM1 | Apoptosis enhanced | PNP | ||
| CCND1 | PDGFRB | Apoptosis reduced | PNP | ||
| TGFB1 | DKK1 | Apoptosis reduced | PNP | ||
| TGFB1 | DNA damage | MAPK8 enhanced | PNP | ||
| E2F1 | AATF | CDK5 enhanced | PNP | ||
| E2F1 | CHEK2 | AATF enhanced | PNP | ||
| E2F1 | CHEK2 | CDK5 enhanced | PNP | ||
| E2F1 | CSNK2 | MYCN enhanced | PNP | ||
| E2F1 | ATM | AATF enhanced | PNP | ||
| E2F1 | ATM | CHEK2 enhanced | PNP | ||
| E2F1 | ATM | CDK5 enhanced | PNP | ||
| E2F1 | ATR | AATF enhanced | PNP | ||
| E2F1 | ATR | CDK5 enhanced | PNP | ||
| E2F1 | DNA damage | AATF enhanced | PNP | ||
| E2F1 | DNA damage | CHEK2 enhanced | PNP | ||
| E2F1 | DNA damage | CDK5 enhanced | PNP | ||
| EGFR | BCL3 | Apoptosis reduced | PNP | ||
| HIF1A | GAPDH | SIAH1 enhanced | PNP | ||
| HIF1A | GAPDH | Apoptosis enhanced | PNP | ||
| HIF1A | SIAH1 | Apoptosis enhanced | PNP | ||
| CXCR4 | TLR3 | Apoptosis enhanced | PNP | ||
| P53 | IFNA1 | TLR3 reduced | [30] | TLR3 enhanced | Opposite to prediction |
This table lists 63 predictions in the selected gene deletion background. Some predictions were verified by existing literature survey or experimental approaches. Potential novel predictions (PNP) indicate that we were unable to identify literature based evidence relevant to the prediction.