Table 3.
Comparison of CASCADE to competing clustering methods for 3 biological network data sets (Yeast DNA damage response network, Rapamycin gene modules network, and Rich medium gene modules network).
| Dataset | Method | Number | Size | Discard(%) | Function (-log p) |
| DNA damage response network | CASCADE | 6 | 15.7 | 5.0 | 2.28 |
| STM | 6 | 16.0 | 5.2 | 2.28 | |
| Quasi clique | 3 | 7.0 | 88.5 | 0.87 | |
| Samanta | 6 | 6.7 | 58.3 | 1.79 | |
| Minimum cut | 7 | 13.1 | 4.2 | 1.18 | |
| Betweenness cut | 10 | 8.8 | 8.3 | 2.22 | |
| MCL | 3 | 9.3 | 70.8 | 2.37 | |
| Chen | 7 | 13.7 | 0.0 | 2.66 | |
| Rives | 5 | 18.4 | 4.1 | 1.61 | |
| SPC | 3 | 20.3 | 36.5 | 2.33 | |
| Rapamycin gene modules network | CASCADE | 4 | 11.8 | 6.0 | 2.90 |
| STM | 4 | 12.5 | 0.0 | 2.57 | |
| Quasi clique | 13 | 8.2 | 0.0 | 2.17 | |
| Samanta | 7 | 4.9 | 32.0 | 1.57 | |
| Minimum cut | 8 | 5.9 | 6.0 | 1.82 | |
| Betweenness cut | 5 | 8.0 | 20.0 | 2.03 | |
| MCL | 6 | 7.7 | 8.0 | 5.48 | |
| Chen | 5 | 10.0 | 0.0 | 2.01 | |
| Rives | 4 | 11.0 | 12.0 | 1.49 | |
| SPC | 3 | 15.3 | 8.0 | 1.47 | |
| Rich medium gene modules network | CASCADE | 4 | 27.8 | 0.0 | 10.5 |
| STM | 5 | 22.4 | 0.0 | 8.21 | |
| Quasi clique | 5 | 22.8 | 0.0 | 7.81 | |
| Samanta | 12 | 5.3 | 43.2 | 4.79 | |
| Minimum cut | 10 | 11.1 | 0.0 | 4.41 | |
| Betweenness cut | 8 | 13.9 | 0.0 | 6.38 | |
| MCL | 23 | 4.0 | 4.5 | 7.29 | |
| Chen | 8 | 13.9 | 0.0 | 6.13 | |
| Rives | 5 | 22.2 | 0.0 | 5.77 | |
| SPC | 5 | 20.6 | 7.2 | 6.80 | |
The Number column indicates the number of clusters identified by each method, the Size column indicates the average number of molecular components in each cluster; the Discard(%) indicates the percentage of molecular components not assigned to any cluster. The average -log p values of all detected clusters for biological function are shown. Comparisons are performed on the clusters with 5 or more molecular components for the first data sets(DNA damage response network), and on the clusters with 3 or more molecular components for the last 2 network data sets(Rapamycin gene modules networks, Rich medium gene modules network). The Maximal clique method is not included in the Table because none of the identified clusters have 3 or more members.