Table 1

Clustering algorithm summary statistics.

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)

Summary statistics detailing Nearest Neighbor Networks clusters formed from the data sets employed in this study, from their concatenation, and from two synthetic random data sets using default parameters (g = 5, n = 25). Results from other clustering algorithms with appropriate output formats (CAST, CLICK, QTC, and SAMBA) have been included, also utilizing default parameter settings provided by the algorithms' implementations. Random values are shown with standard deviations over five different seeds.

Huttenhower et al. BMC Bioinformatics 2007 8:250   doi:10.1186/1471-2105-8-250