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Table 9 Comparisons between the different methods on the ICD(Gavin+Krogan) network

From: MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

  

Method

  

MCL

MCLO

MCL-CAw

CMC

HACO

 

#Predicted

136

121

129

171

104

Wodak

(#153)

#Matched

68

73

80

86

68

 

Precision

0.500

0.603

0.620

0.503

0.654

 

#Derived

76

73

80

86

76

 

Recall

0.497

0.477

0.523

0.562

0.497

MIPS'

(#151)

#Matched

47

56

63

65

41

 

Precision

0.346

0.463

0.488

0.380

0.394

 

#Derived

60

56

63

65

55

 

Recall

0.397

0.371

0.417

0.430

0.364

Aloy

(#75)

#Matched

58

56

59

59

53

 

Precision

0.426

0.463

0.457

0.345

0.510

 

#Derived

56

56

59

59

53

 

Recall

0.747

0.747

0.787

0.787

0.707

  1. Methods considered: MCL, MCLO, MCL-CAw, CMC and HACO. HACO performed the best in terms of precision, while CMC performed the best in terms of recall. MCL-CAw was a close second in both precision and recall. #Matched: #Predictions matching some benchmark complex(es). #Derived: #Benchmark complexes derived by some predicted complex(es).
  2. The ICD(Gavin+Krogan) network
  3. #Proteins 1628; #Interactions 8707
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BMC Bioinformatics

ISSN: 1471-2105

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