Table 1

Clustering algorithm summary statistics.

NNN g = 5, n = 25

CAST t = 0.8

CLICK h = μ_T

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