Table 1. Simulation studies of co-expression cluster detection.
Conditions with optimal performance are highlighted in red.
| % top proteins for analysis | # simulated modules | # detected modules | # recaptured modules1 | precision2 | recall3 |
|---|---|---|---|---|---|
| Highly dynamic proteome (e.g., during T cell activation): 6 simulated modules from 50% proteome | |||||
|
| |||||
| 2 | 6 | 2 | 2 | 1 | 0.33 |
| 5 | 6 | 2 | 2 | 1 | 0.33 |
| 10 | 6 | 3 | 3 | 1 | 0.5 |
| 20 | 6 | 4 | 4 | 1 | 0.67 |
| 50 | 6 | 6 | 6 | 1 | 1 |
| 100 | 6 | 8 | 5 | 0.63 | 0.83 |
|
| |||||
| Relatively stable proteome (e.g., during pathogenesis of AD): 3 simulated modules from 2% proteome | |||||
|
| |||||
| 1 | 3 | 1 | 1 | 1 | 0.33 |
| 2 | 3 | 3 | 3 | 1 | 1 |
| 5 | 3 | 8 | 3 | 0.38 | 1 |
| 10 | 3 | 13 | 3 | 0.23 | 1 |
| 20 | 3 | 19 | 3 | 0.16 | 1 |
| 50 | 3 | 71 | 2 | 0.03 | 0.67 |
| 100 | 3 | 169 | 2 | 0.01 | 0.67 |
1
A recaptured module is a detected module whose eigengene highly correlates (Pearson R > 0.95) with one of the simulated eigengenes.
2
precision = # recaptured modules / # detected modules
3
recall = # recaptured modules / # simulated modules