Table 2.
Biclique prediction performance with different minimum number of compounds (c) and proteins (p)
| Biclique size | # PI | # TP | TPR | # FP | FPR | PPV | TP/PI |
|---|---|---|---|---|---|---|---|
| c: 8, p: 4 | 91 | 65 | 0.10 | 2 | 0.00 | 0.97 | 0.71 |
| c: 8, p: 3 | 122 | 80 | 0.13 | 3 | 0.00 | 0.96 | 0.66 |
| c: 5, p: 3 | 1295 | 206 | 0.33 | 121 | 0.01 | 0.63 | 0.16 |
| c: 5, p: 2 | 1994 | 248 | 0.39 | 171 | 0.02 | 0.59 | 0.12 |
Note: The number of edges represents the number of predicted interactions. PI, predicted interactions, TP/PI provides an estimation of the expected validation success when tested experimentally. Chosen data correspond to bicliques with associated mean FPRs below 0.05, nrepeats =10. PPV, positive predictive value. Two large bicliques (c: 8, p: 4/3) and two middle sized bicliques (c: 5, p: 3/2) are listed, including the biclique size, which was identified as the optimum (c: 5, p: 2). For a complete data table, see Supplementary Table S3.