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Table 5 Function enrichment analysis of protein complexes detected from different datasets

From: Identifying protein complexes based on an edge weight algorithm and core-attachment structure

Dataset

Algorithms

PC

<E-15

[E-15,E-10)

[E-10,E-5)

[E-5,0.01)

Significant

BioGRID

CMC

1113

125(11.23%)

89(7.99%)

258(23.18%)

360(32.34%)

832(74.76%)

 

PEWCC

387

181(46.77%)

64(16.53%)

83(21.44%)

46(11.88%)

374(96.65%)

 

GMFTP

597

73(12.22%)

59(9.88%)

156(26.13%)

161(26.96%)

449(75.21%)

 

COACH

166

76(45.78%)

32(19.27%)

38(22.89%)

16(9.63%)

162(97.60%)

 

ProRank+

746

479(64.20%)

105(14.07%)

97(13.00%)

47(6.30%)

18(97.59%)

 

DPC

2167

596(27.50%)

166(7.66%)

290(13.38%)

569(26.25%)

1621(74.81%)

 

EWCA

1388

658(47.40%)

211(15.20%)

299(21.54%)

173(12.46%)

1341(96.62%)

DIP

CMC

303

1(0.33%)

8(2.64%)

58(19.14%)

77(25.41%)

144(47.53%)

 

PEWCC

676

78(11.53%)

117(17.30%)

278(41.12%)

132(19.52%)

605(89.50%)

 

GMFTP

548

43(7.84%)

36(6.56%)

105(19.16%)

166(30.29%)

350(63.69%)

 

COACH

329

21(6.38%)

25(7.59%)

66(20.06%)

32(9.72%)

144(43.68%)

 

ProRank+

338

74(21.89%)

77(22.78%)

126(37.27%)

42(12.42%)

319(94.38%)

 

DPC

622

72(11.57%)

113(18.16%)

197(31.67%)

176(28.29%)

558(89.72%)

 

EWCA

964

188(19.50%)

126(13.07%)

319(33.09%)

236(24.48%)

870(90.15%)

  1. NOTE: Table 5 lists the number percentage of protein complexes detected by CMC, PEWCC, GMFTP, COACH, ProRank+, DPC and EWCA in the PPI network whose p-value falls within different value ranges. In order to analyze functional enrichment, we should take into account of two values. For example, in the DIP dataset, in the fourth column of the fourteenth row 188 times 19.50% is 36.66 which is the highest value in this column that means EWCA is the best among these methods. Here, from the fourth column to the seventh column the larger value is, the better functional enrichment is