Table 1

Summary of MCODE Results with Best Parameters on Various Data Sets.

Data Set

Number of Proteins

Number of Interact-ions

Number of Predicted Complexes

MCODE Complexes Predicted Above ω = 0.2

Matched Benchmark Complexes

Complex Benchmark

Best MCODE Parameters


Gavin Spoke

1363

3225

82

63

88

Gavin

hFfT\0.05\0.05

Gavin Spoke

1363

3225

53

20

20

MIPS

hTfT\0.1\0.35

Pre HTMS

4379

9088

158

21

28

Gavin

hTfT\0\0.2\

Pre HTMS

4379

9088

166

52

64

MIPS

hTfT\0.1\0.2

AllYeast

4825

15143

209

52

76

Gavin

hFfT\0\0.1

AllYeast

4825

15143

209

54

63

MIPS

hTfT\0\0.1

AllYeast

4825

15143

203

80

150

MIPS+Gavin

hTfT\0\0.15\

Benchmark

1762

3310

141

23

30

Gavin

hTfT\0\0.3

Benchmark

1762

3310

163

58

67

MIPS

hTfT\0.1\0.05

HTP Only

4557

12249

138

46

77

Gavin

hTfT\0.05\0.1

HTP Only

4557

12249

122

29

35

MIPS

hTfT\0.05\0.15

Y2H

3847

6133

73

7

7

Gavin

hTfT\0.2\0.1

Y2H

3847

6133

78

21

26

MIPS

hTfT\0\0.1


Statistics and a summary of results are shown for the various data sets used to evaluate MCODE. 'Gavin Spoke' is the Gavin et al. data set represented as binary interactions using the spoke model; 'Pre HTMS' is the set of all yeast interaction not including the recent high-throughput mass spectrometry studies [6,7].; 'AllYeast' is the set of all yeast interactions that we could collect; 'Benchmark' is a set of interactions found in the literature from YPD, MIPS and PreBIND; 'HTP Only' is the combination of all large-scale and high-throughput yeast two-hybrid and mass spectrometry data sets; 'Y2H' is the set of all yeast two-hybrid results from large-scale and literature sources. See Methods for full explanation of data sets. The 'Best MCODE Parameters' are formatted as haircut True of False, fluff True or False\VWP\Fluff Density Threshold Parameter.

Bader and Hogue BMC Bioinformatics 2003 4:2   doi:10.1186/1471-2105-4-2

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