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Table 10 Comparisons between the different methods on the FSW(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

120

108

117

176

99

Wodak

(#153)

#Matched

69

61

72

76

68

 

Precision

0.575

0.564

0.615

0.432

0.687

 

#Derived

78

72

83

84

77

 

Recall

0.510

0.471

0.542

0.549

0.503

MIPS

(#151)

#Matched

46

42

48

49

42

 

Precision

0.383

0.388

0.410

0.278

0.424

 

#Derived

61

55

66

65

56

 

Recall

0.404

0.364

0.437

0.430

0.371

Aloy

(#75)

#Matched

57

56

60

59

53

 

Precision

0.475

0.518

0.513

0.335

0.535

 

#Derived

57

56

60

57

53

 

Recall

0.760

0.747

0.800

0.760

0.707

  1. Methods considered: MCL, MCLO, MCL-CAw, CMC and HACO. HACO performed the best in terms of precision, while MCL-CAw and CMC performed the best in terms of recall. MCL-CAw was a close second in terms of precision. #Matched: #Predictions matching some benchmark complex(es). #Derived: #Benchmark complexes derived by some predicted complex(es).
  2. The FSW(Gavin+Krogan) network
  3. #Proteins 1628; #Interactions 8688