Table 6 Subnetworks of breast cancer data. The BC-1nb-net/BC-2nb-net had 294/1,718 genes in total including 40/107 cancer genes, and 7/14 cancer genes with mutation frequencies larger than 0.10. The classification error, number of selected cancer genes with mutation frequencies larger than 0.10 (CA-LMF), number of selected cancer genes (CA), number of selected genes, and their standard errors (SE in parentheses) were obtained by averaging over 10 runs.
From: Network-based support vector machine for classification of microarray samples
Network | Method | Error | # CA-LMF | # CA | # Genes |
|---|---|---|---|---|---|
BC-1nb-net | STD | 0.371 (0.014) | 7.0 (0.0) | 40.0 (0.0) | 294.0 (0.0) |
L1 | 0.357 (0.014) | 0.3 (0.2) | 4.6 (0.8) | 32.3 (4.8) | |
New (w = 1) | 0.360 (0.014) | 0.4 (0.2) | 3.6 (1.1) | 25.0 (7.0) | |
New (w = ) | 0.366 (0.012) | 0.6 (0.3) | 4.7 (1.2) | 27.2 (5.2) | |
New (w = d) | 0.399 (0.012) | 1.2 (0.2) | 7.8 (1.7) | 40.2 (6.5) | |
Final Model | - | 1.0 | 4.0 | 14.0 | |
BC-2nb-net | STD | 0.351 (0.014) | 14.0 (0.0) | 107.0 (0.0) | 1,718.0 (0.0) |
L1 | 0.360 (0.006) | 0.0 (0.0) | 2.4 (0.9) | 42.9 (11.8) | |
New (w = 1) | 0.374 (0.011) | 0.1 (0.1) | 1.9 (0.5) | 51.4 (12.6) | |
New (w = ) | 0.360 (0.007) | 0.2 (0.1) | 2.5 (0.7) | 41.7 (9.2) | |
New (w = d) | 0.385 (0.021) | 0.3 (0.2) | 0.7 (0.3) | 34.2 (10.3) | |
Final Model | - | 1.0 | 2.0 | 23.0 |