Table 2:
Extracting core subsets for p53 cell-lines
| Gene set | Gene-set size | Core pathway size | Percent reduction | Core pathway members (SAM-GS P-values) |
|---|---|---|---|---|
| ATM Pathway | 19 | 2 | 89.5 | CDKN1A (0.001), MDM2 (0.001) |
| BAD Pathway | 21 | 2 | 90.5 | BAX (0.001), BCL2 (0.001) |
| bcl2family & reg. network | 23 | 1 | 95.7 | BAX (0.001) |
| Calcineurin pathway | 18 | 1 | 94.4 | CDKN1A (0.001) |
| Cell cycle regulator | 23 | 2 | 91.3 | CDKN1A (0.001), BTG2(0.002) |
| D _DAMAGE_SIG_LLING | 90 | 5 | 94.4 | CDKN1A (0.001), BAX (0.001), DDB2 (0.001), MDM2 (0.001), BTG2 (0.003) |
| drug_resistance_and_metabolism | 95 | 2 | 97.9 | CDKN1A (0.001), BAX (0.001) |
| g2 pathway | 23 | 2 | 91.3 | CDKN1A (0.001), MDM2 (0.001) |
| hsp27 pathway | 15 | 4 | 73.3 | FAS (0.001), TNFRSF6 (0.001), BCL2 (0.002), IL1A (0.002) |
| p53 signaling | 87 | 3 | 96.6 | CDKN1A (0.001), BAX (0.001), MDM2 (0.001) |
| p53hypoxia pathway | 20 | 3 | 85.0 | CDKN1A (0.001), BAX (0.001), MDM2(0.001) |
| p53 Pathway | 16 | 3 | 81.3 | CDKN1A (0.001), BAX (0.001), MDM2 (0.001) |
| Raccycd pathway | 22 | 1 | 95.5 | CDKN1A (0.001) |
| radiation_sensitivity | 26 | 3 | 88.5 | CDKN1A (0.001), BAX (0.001), MDM2 (0.001) |
| SA_TRKA_RECEPTOR | 16 | 1 | 93.8 | CDKN1A (0.001) |
| P53_UP | 40 | 5 | 87.5 | CDKN1A (0.001), BAX (0.001), DDB2 (0.001), MDM2 (0.001), BTG2 (0.003) |
| breast_cancer_estrogen_sig lling | 97 | 3 | 96.9 | CDKN1A (0.001), TNFRSF6 (0.001), ESR2 (0.003) |
| Ceramide pathway | 22 | 1 | 95.5 | BAX (0.001) |
| CR_DEATH | 70 | 1 | 98.6 | BAX (0.001) |
| Mitochondria pathway | 19 | 1 | 94.7 | BAX (0.001) |
| g1 pathway | 26 | 1 | 96.2 | CDKN1A (0.001) |
| SIG_IL4RECEPTOR_IN_B_LYPHOCYTES | 26 | 1 | 96.2 | STAT6 (0.001) |
| ST_Interleukin_4_Pathway | 24 | 1 | 95.8 | STAT6 (0.001) |
| ets pathway | 16 | 2 | 87.5 | SIN3B (0.003), CSF1R (0.004) |
| ca_nf_at_sig lling | 95 | 2 | 97.9 | CDKN1A (0.001), BCL2 (0.002) |
| cell_cycle_arrest | 30 | 1 | 96.7 | CDKN1A (0.001) |
| Cellcycle pathway | 23 | 1 | 95.7 | CDKN1A (0.001) |
| Chemical pathway | 21 | 1 | 95.2 | BAX (0.001) |
| ST_Fas_Sig ling_Pathway | 56 | 1 | 98.2 | BAX (0.001) |
| Cytokine pathway | 21 | 2 | 90.5 | IL1A (0.002), IFNA1(0.005) |
| Hivnef pathway | 54 | 2 | 96.3 | MDM2 (0.001), TNFRSF6 (0.001) |
Core subsets extracted by SAM-GSR, for 31 sets significant at 0.01, using a cutoff c = 0.1 for ck values.