Table 2.
Comparison of predictive accuracy resulted from different screening methods
| Minimum required interaction score | Methods | Hub genes | k | Accuracy of kNN algorithm | Mean accuracy of random forest algorithm (rerun 100 times) |
|---|---|---|---|---|---|
| 0.700 | Method 1: 724 DGEs-181 candidate genes-genes bearing top 10 degrees in PPI-2 hub genes by survival analysis and cox analysis | MMP7, ITGA2 | 2 | 78.21% | 81.31% |
| 5 | 84.62% | ||||
| 10 | 87.18% | ||||
| 23 | 92.31% | ||||
| 27 | 93.59% | ||||
| Method 2: 724 DGEs-181 candidate genes-genes bearing top 10 degrees in PPI | ALB, EGF, FN1, ITGA2, COL1A2, SPARC, COL3A1, TIMP1, COL5A1, COL11A1, MMP7 | 2 | 79.49% | 83.54% | |
| 4 | 70.51% | ||||
| 6 | 76.92% | ||||
| 9 | 78.20% | ||||
| 13 | 80.77% | ||||
| 15 | 88.46% | ||||
| 18 | 83.33% | ||||
| Method 3: 724 DGEs-genes bearing top 10 degrees in PPI-2 hub genes by survival analysis and cox analysis | TOP2A, MAD2L1 | 2 | 65.38% | 69.82% | |
| 5 | 69.23% | ||||
| 8 | 65.38% | ||||
| 12 | 66.67% | ||||
| 23 | 67.95% | ||||
| Method 4: 724 DGEs-genes bearing top 10 degrees in PPI | CCNB1, CCNA2, MAD2L1, TOP2A, UBE2C, CDC20, TTK, MELK, BUB1B, NDC80 | 2 | 70.51% | 74.81% | |
| 5 | 71.80% | ||||
| 8 | 76.92% | ||||
| 13 | 75.64% | ||||
| 23 | 74.36% | ||||
| 0.400 | Method 5: 724 DGEs-181 candidate genes-genes bearing top 10 degrees in PPI-1 hub genes by survival analysis and cox analysis | ITGA2 | 2 | 74.36% | 69.23% |
| 5 | 80.77% | ||||
| 10 | 80.77% | ||||
| 14 | 80.77% | ||||
| 18 | 82.05% | ||||
| 22 | 85.90% | ||||
| Method 6: 724 DGEs-181 candidate genes-genes bearing top 10 degrees in PPI | ALB, EGF, ITGA2, FN1, COL1A2, TIMP1, MMP1, COL3A1, PTGS2, CEL | 2 | 82.05% | 83.72% | |
| 4 | 71.80% | ||||
| 6 | 79.49% | ||||
| 10 | 75.64% | ||||
| 13 | 74.36% | ||||
| 18 | 73.08% | ||||
| Method7:724 DGEs-genes bearing top10 degrees in PPI-2 hub genes by survival analysis and cox analysis | TOP2A, MAD2L1 | 2 | 65.38% | 69.82% | |
| 5 | 69.23% | ||||
| 8 | 65.38% | ||||
| 12 | 66.67% | ||||
| 23 | 67.95% | ||||
| Method8:724 DGEs-genes bearing top 10 degrees in PPI | ALB, GAPDH, EGF, TOP2A, CCNB1, NDC80, CCNA2, CDC20, UBE2C, BUB1B, MAD2L1, TTK, OIP5, KIF11 | 2 | 71.79% | 73.05% | |
| 6 | 73.08% | ||||
| 11 | 69.23% | ||||
| 15 | 70.51% | ||||
| 22 | 73.08% |
Method 1: Identification of DEGs → screening candidate genes with top 25% variance → construction of PPI by candidate genes with minimum required interaction score at 0.700, and further screen candidate genes with top 10 degrees in PPI → Selection of hub genes by survival and cox analyses in TCGA database
Method 2: Identification of DEGs → screening candidate genes with top 25% variance → construction of PPI by candidate genes with minimum required interaction score at 0.700, and further identification of hub genes bearing top 10 degrees in PPI
Method 3: Identification of DEGs → construction of PPI by candidate genes with minimum required interaction score at 0.700, and further screen candidate genes with top 10 degrees in PPI → selection of hub genes by survival and cox analyses in TCGA database
Method 4: Identification of DEGs → construction of PPI by candidate genes with minimum required interaction score at 0.700, and further identification of hub genes bearing top 10 degrees in PPI
Method 5: Identification of DEGs → screening candidate genes with top 25% variance → construction of PPI by candidate genes with minimum required interaction score at 0.400, and further screen candidate genes with top 10 degrees in PPI → selection of hub genes by survival and cox analyses in TCGA database
Method 6: Identification of DEGs → screening candidate genes with top 25% variance → construction of PPI by candidate genes with minimum required interaction score at 0.400, and further identification of hub genes bearing top 10 degrees in PPI
Method 7: Identification of DEGs → construction of PPI by candidate genes with minimum required interaction score at 0.400, and further screen candidate genes with top 10 degrees in PPI → selection of hub genes by survival and cox analyses in TCGA database
Method 8: Identification of DEGs → construction of PPI by candidate genes with minimum required interaction score at 0.400, and further identification of hub genes bearing top 10 degrees in PPI