From: Evaluation of clustering algorithms for protein-protein interaction networks
Dataset | Nb nodes | Nb edges | Mean degree | Mean clust coeff | Â | MCL | MCODE | RNSC | SPC | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
 |  |  |  |  |  | real | permuted | real | permuted | real | permuted | real | permuted |
Uetz et al. [1] | 926 | 865 | 1.175 | 0.018 | Number of clusters | 288 | 10 | 48 | 234 | ||||
 |  |  |  |  | Mean nb prot/cluster | 3.22 | 11.2 | 1.91 | 3.96 | ||||
 |  |  |  |  | Median nb prot/cluster | 3 | 4.5 | 2 | 2 | ||||
 |  |  |  |  | Largest cluster size | 16 | 53 | 6 | 276 | ||||
 |  |  |  |  | Sn | 57.3% | 38.6% | 84.3% | 74.5% | 49.4% | 36.5% | 65.5% | 43.3% |
 |  |  |  |  | PPV | 53.8% | 45.9% | 25.5% | 21.6% | 59.6% | 54.4% | 38.0% | 38.9% |
 |  |  |  |  | Acc g | 55.6% | 42.3% | 54.9% | 48.0% | 54.5% | 45.5% | 51.8% | 41.1% |
 |  |  |  |  | Sep co | 23.0% | 20.6% | 48.9% | 62.5% | 15.5% | 14.8% | 19.1% | 21.2% |
 |  |  |  |  | Sep cl | 30.1% | 26.9% | 2.2% | 2.8% | 34.3% | 32.7% | 20.3% | 22.6% |
 |  |  |  |  | Sep | 26.3% | 23.5% | 10.4% | 13.3% | 23.1% | 22.0% | 19.7% | 21.9% |
Ito et al. [2] | 2937 | 4038 | 2.682 | 0.019 | Number of clusters | 630 | 9 | 1746 | 410 | ||||
 |  |  |  |  | Mean nb prot/cluster | 4.66 | 97.8 | 1.68 | 7.16 | ||||
 |  |  |  |  | Median nb prot/cluster | 3 | 11 | 2 | 2 | ||||
 |  |  |  |  | Largest cluster size | 157 | 485 | 4 | 1928 | ||||
 |  |  |  |  | Sn | 34.9% | 26.0% | 66.9% | 68.0% | 31.4% | 24.0% | 73.2% | 64.6% |
 |  |  |  |  | PPV | 42.7% | 38.5% | 8.2% | 5.8% | 63.6% | 61.8% | 24.3% | 23.8% |
 |  |  |  |  | Acc g | 38.8% | 32.2% | 37.5% | 36.9% | 47.5% | 42.9% | 48.8% | 44.2% |
 |  |  |  |  | Sep co | 12.7% | 11.8% | 41.6% | 33.0% | 7.1% | 7.0% | 11.3% | 11.0% |
 |  |  |  |  | Sep cl | 36.2% | 33.9% | 1.7% | 1.3% | 56.7% | 55.9% | 20.1% | 20.4% |
 |  |  |  |  | Sep | 21.4% | 20% | 8.4% | 6.7% | 20.1% | 19.8% | 15.4% | 15.0% |
Ho et al. [5] | 1564 | 3600 | 4.6 | 0.029 | Number of clusters | 314 | 13 | 957 | 63 | ||||
 |  |  |  |  | Mean nb prot/cluster | 4.98 | 49.5 | 1.63 | 24.8 | ||||
 |  |  |  |  | Median nb prot/cluster | 3 | 13 | 1 | 3 | ||||
 |  |  |  |  | Largest cluster size | 34 | 432 | 8 | 1383 | ||||
 |  |  |  |  | Sn | 50.6% | 28.2% | 81.2% | 76.5% | 37.0% | 27.4% | 90.1% | 92.1% |
 |  |  |  |  | PPV | 47.1% | 35.6% | 12.9% | 8.5% | 61.5% | 57.1% | 10.4% | 8.2% |
 |  |  |  |  | Acc g | 48.9% | 31.9% | 47.1% | 42.5% | 49.3% | 42.2% | 50.2% | 50.2% |
 |  |  |  |  | Sep co | 22.6% | 19% | 44.7% | 37.2% | 11% | 10.5% | 19.3% | 13.8% |
 |  |  |  |  | Sep cl | 32.3% | 27.1% | 2.6% | 2.2% | 48% | 45.6% | 5.5% | 4.0% |
 |  |  |  |  | Sep | 27.0% | 22.7% | 10.9% | 9.0% | 23% | 21.9% | 10.3% | 7.4% |
Gavin et al. [4] | 1352 | 3210 | 4.7 | 0.148 | Number of clusters | 212 | 27 | 709 | 87 | ||||
 |  |  |  |  | Mean nb prot/cluster | 6.38 | 32.5 | 1.91 | 15.5 | ||||
 |  |  |  |  | Median nb prot/cluster | 4 | 7 | 1 | 2 | ||||
 |  |  |  |  | Largest cluster size | 54 | 414 | 16 | 1074 | ||||
 |  |  |  |  | Sn | 74.1% | 24.2% | 67.0% | 51.1% | 52.1% | 20.8% | 91.8% | 81.4% |
 |  |  |  |  | PPV | 57.0% | 23.9% | 20.4% | 9.4% | 62.0% | 46.0% | 18.1% | 10.7% |
 |  |  |  |  | Acc g | 65.6% | 24.0% | 43.7% | 30.3% | 57.1% | 33.4% | 54.9% | 46.0% |
 |  |  |  |  | Sep co | 39.4% | 17.6% | 44.5% | 16.1% | 14.5% | 11.3% | 34.4% | 15.7% |
 |  |  |  |  | Sep cl | 38.0% | 17.0% | 5.5% | 2.0% | 46.9% | 36.5% | 13.6% | 6.2% |
 |  |  |  |  | Sep | 38.7% | 17.3% | 15.6% | 5.6% | 26.1% | 20.3% | 21.6% | 9.8% |
Gavin et al. [6] | 1430 | 6531 | 9.1 | 0.348 | Number of clusters | 189 | 39 | 487 | 136 | ||||
 |  |  |  |  | Mean nb prot/cluster | 7.57 | 40.3 | 2.94 | 10.5 | ||||
 |  |  |  |  | Median nb prot/cluster | 4 | 9 | 2 | 3 | ||||
 |  |  |  |  | Largest cluster size | 90 | 697 | 35 | 620 | ||||
 |  |  |  |  | Sn | 75.7% | 23.7% | 58.3% | 43.2% | 60.8% | 20.9% | 79.8% | 48.4% |
 |  |  |  |  | PPV | 54.3% | 21.0% | 20.6% | 8.0% | 63.3% | 37.3% | 37.0% | 16.5% |
 |  |  |  |  | Acc g | 65.0% | 22.4% | 39.5% | 25.6% | 62.1% | 29.1% | 58.4% | 32.4% |
 |  |  |  |  | Sep co | 38.1% | 15.5% | 44.7% | 15.3% | 20.1% | 12.9% | 34.9% | 14.9% |
 |  |  |  |  | Sep cl | 32.7% | 13.3% | 7.9% | 2.7% | 44.5% | 28.6% | 21.6% | 9.2% |
 |  |  |  |  | Sep | 35.3% | 14.4% | 18.8% | 6.4% | 29.9% | 19.2% | 27.4% | 11.7% |
Krogan et al. [7] | 2675 | 7088 | 5.296 | 0.146 | Number of clusters | 813 | 70 | 1405 | 114 | ||||
 |  |  |  |  | Mean nb prot/cluster | 4.93 | 28.3 | 2.1 | 10.3 | ||||
 |  |  |  |  | Median nb prot/cluster | 3 | 5.5 | 2 | 3 | ||||
 |  |  |  |  | Largest cluster size | 50 | 387 | 21 | 1724 | ||||
 |  |  |  |  | Sn | 62.8% | 19.8% | 56.3% | 30.9% | 53.1% | 19.1% | 82.6% | 64.0% |
 |  |  |  |  | PPV | 56.2% | 33.5% | 21.9% | 9.7% | 63.3% | 51.1% | 25.4% | 17.2% |
 |  |  |  |  | Acc g | 59.5% | 26.7% | 39.1% | 20.3% | 58.2% | 35.1% | 54.0% | 40.6% |
 |  |  |  |  | Sep co | 20.0% | 12.1% | 33.2% | 13.6% | 10.3% | 8.7% | 20.3% | 11.9% |
 |  |  |  |  | Sep cl | 49.5% | 29.9% | 8.8% | 3.6% | 59.6% | 50.3% | 24.0% | 14.1% |
 |  |  |  |  | Sep | 31.5% | 19.0% | 17.0% | 7.0% | 24.7% | 21.6% | 20.9% | 12.9% |