Table 1 Clustering algorithm summary statistics.
From: Nearest Neighbor Networks: clustering expression data based on gene neighborhoods
|  | NNN g = 5, n = 25 | CAST t = 0.8 | CLICK h = μT | QTC d = 0.5, n = 5 | SAMBA |
|---|---|---|---|---|---|
Brem 2005, 6162 genes, 131 conditions | |||||
Genes | 1527 | 3410 | 6162 | 6137 | 2284 |
Clusters | 54 | 800 | 82 | 127 | 113 |
Mean Size | 28.4 | 4.26 | 75.1 | 48.3 | 102 |
Size Dev. | 49.2 | 16.91 | 161 | 93.3 | 70.3 |
Gasch 2000, 6115 genes, 173 conditions | |||||
Genes | 1142 | 4079 | 6115 | 6092 | 3120 |
Clusters | 38 | 666 | 9 | 69 | 128 |
Mean Size | 30.1 | 6.12 | 679 | 88.3 | 130 |
Size Dev. | 62.5 | 35.58 | 787 | 220 | 101 |
Haugen 2004, 6256 genes, 7 conditions | |||||
Genes | 64 | 6251 | 6256 | 6236 | 280 |
Clusters | 11 | 45 | 16 | 56 | 5 |
Mean Size | 5.82 | 138.9 | 391 | 11.4 | 88.4 |
Size Dev. | 1.19 | 347.3 | 474 | 258 | 36.5 |
Hughes 2000, 6153 genes, 300 conditions | |||||
Genes | 1996 | 2579 | 6153 | 6121 | 3375 |
Clusters | 29 | 519 | 75 | 177 | 325 |
Mean Size | 68.9 | 4.97 | 82.0 | 34.6 | 45.9 |
Size Dev. | 245.4 | 11.95 | 107 | 57.8 | 44.1 |
Primig 2000, 6005 genes, 24 conditions | |||||
Genes | 2247 | 5820 | 6005 | 5970 | 778 |
Clusters | 27 | 687 | 46 | 110 | 25 |
Mean Size | 83.2 | 8.47 | 131 | 54.3 | 139 |
Size Dev. | 390 | 19.26 | 187 | 80.4 | 96.3 |
Spellman 1998, 5701 genes, 25 conditions | |||||
Genes | 2050 | 5535 | 5701 | 5669 | 777 |
Clusters | 28 | 616 | 47 | 100 | 32 |
Mean Size | 73.3 | 8.99 | 121 | 56.7 | 69.0 |
Size Dev. | 324 | 30.14 | 206 | 114 | 37.3 |
Concatenated Data, 6160 genes, 660 conditions | |||||
Genes | 694 | 6155 | 6160 | - | 4892 |
Clusters | 29 | 7 | 5 | - | 609 |
Mean Size | 23.9 | 879.3 | 1232 | - | 63.7 |
Size Dev. | 34.7 | 2140 | 1768 | - | 82.0 |
Uniformly Distributed Random Data, 6000 genes, 10 conditions | |||||
Genes | 0 (± 0) | 5988 (± 0.89) | 3600 (± 3286) | 5964 (± 28.8) | 0 (± 0) |
Clusters | 0 (± 0) | 216.2 (± 2.95) | 9.8 (± 9.81) | 109 (± 4.72) | 0 (± 0) |
Mean Size | 0 (± 0) | 27.7 (± 0.38) | 190 (± 175) | 53.0 (± 1.39) | 0 (± 0) |
Size Dev. | 0 (± 0) | 21.86 (± 0.25) | 48.8 (± 45.7) | 35.2 (± 0.791) | 0 (± 0) |
Normally Distributed Random Data, 6000 genes, 10 conditions | |||||
Genes | 0 (± 0) | 5986 (± 3.58) | 6000 (± 0) | 5975 (± 4.77) | 0 (± 0) |
Clusters | 0 (± 0) | 231.6 (± 3.29) | 28.8 (± 11.9) | 124 (± 1.30) | 0 (± 0) |
Mean Size | 0 (± 0) | 25.85 (± 0.36) | 235 (± 82.6) | 48.3 (± 0.482) | 0 (± 0) |
Size Dev. | 0 (± 0) | 18.14 (± 0.15) | 64.8 (± 46.3) | 30.9 (± 0.374) | 0 (± 0) |
Brem 2005, 6162 genes, 131 conditions, randomly permuted | |||||
Genes | 101.4 (± 28.85) | 0 (± 0) | 6162 (± 0) | 5837 (± 260.6) | 1061 (± 35.87) |
Clusters | 16.2 (± 3.96) | 0 (± 0) | 36.2 (± 28.99) | 428 (± 33.88) | 156 (± 4.85) |
Mean Size | 6.23 (± 0.78) | 0 (± 0) | 680.7 (± 864.7) | 13.67 (± 0.46) | 32.46 (± 1.35) |
Size Dev. | 1.64 (± 0.79) | 0 (± 0) | 884.5 (± 1179) | 2.36 (± 0.52) | 18.03 (± 1.13) |
Gasch 2000, 6115 genes, 173 conditions, randomly permuted | |||||
Genes | 19.4 (± 6.66) | 0 (± 0) | 4586 (± 3058) | 5507 (± 47.19) | 1382 (± 15.27) |
Clusters | 3.6 (± 1.34) | 0 (± 0) | 20.75 (± 33.71) | 411.2 (± 5.12) | 219.8 (± 15.27) |
Mean Size | 5.47 (± 1.04) | 0 (± 0) | 701 (± 941.3) | 13.39 (± 0.058) | 18.38 (± 0.35) |
Size Dev. | 0.66 (± 1.48) | 0 (± 0) | 950.8 (± 1197) | 1.7 (± 0.03) | 9.25 (± 0.38) |
Hughes 2000, 6153 genes, 300 conditions, randomly permuted | |||||
Genes | 20.2 (± 8.61) | 572.8 (± 12.74) | 4922 (± 2752) | 4815 (± 76.96) | 1808 (± 56.32) |
Clusters | 3.6 (± 1.82) | 224 (± 8.22) | 13 (± 10.84) | 407.2 (± 7.56) | 390.8 (± 5.67) |
Mean Size | 6.13 (± 1.64) | 2.56 (± 0.044) | 592.5 (± 826.8) | 11.83 (± 0.038) | 11.09 (± 0.39) |
Size Dev. | 0.53 (± 0.71) | 0.82 (± 0.046) | 101.7 (± 200.2) | 1.15 (± 0.024) | 5.59 (± 0.5) |