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Table 6 Main features of the four large scale data sets and clustering performances of the algorithms when applied to them

From: Evaluation of clustering algorithms for protein-protein interaction networks

Dataset Nb nodes Nb edges Mean degree Mean clust coeff   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%