Table 2.
Subnetworks identified by seven methods applied to bladder cancer and head and neck cancer data. hHotNet: Hierarchical HotNet. #subnetworks: the number of identified subnetworks; #genes: the total number of genes in identified subnetworks; # COSMIC genes: the number of genes that are included in the COSMIC cancer gene database.
| Bladder Cancer | Head and Neck Cancer | ||||||
|---|---|---|---|---|---|---|---|
| Method | #Genes | #Subnetworks | FDR | #COSMIC Genes |
#Genes | #Subnetworks | FDR |
| MultiFDRnet | 77 | 24 | 0.084(0.01) | 29 | 61 | 16 | 0.083(0.01) |
| FDRnet | 95 | 28 | 0.086(0.01) | 30 | 77 | 15 | 0.093(0.006) |
| hHotNet | 22 | 1 | 0.028 | 17 | 33 | 2 | 0.06(0.05) |
| HotNet2 | 52 | 1 | 0.17 | 28 | 56 | 1 | 0.05 |
| Domino | 27 | 3 | 0.54(0.16) | 10 | 110 | 15 | 0.50(0.18) |
| NetMix2 | 21 | 1 | 0.18 | 17 | 20 | 1 | 0.07 |
| BioNet | / | / | / | / | / | / | / |