Table 4

MCL-CAw performed considerably better than MCL in the presence of natural noise

PPI Network

#Proteins

#Interactions

Avg node deg

#Derived MCL

complexes (Recall) MCL-CAw


Consol3.19

1622

9704

11.96

79 (0.545)

82 (0.566)

Consol0.623

5423

102393

37.76

74 (0.321)

84 (0.375)


ICD(Cons3.19)

1161

8688

14.96

58 (0.408)

63 (0.443)

ICD(Cons0.623)

1273

19996

31.41

52 (0.353)

56 (0.381)


FSW(Cons3.19)

1123

8694

15.48

59 (0.401)

65 (0.442)

FSW(Cons0.623)

1341

20696

30.87

54 (0.360)

57 (0.380)


The Consolidated3.19 and Consolidated0.623 networks were subsets of the Consolidated network [11] derived with PE cut-offs 3.19 and 0.623, respectively. We ran ICD and FSW schemes on these networks. Consolidated0.623 had significant amount of false positives (about 81%) that were discarded by the scoring. The performance of MCL-CAw was only marginally better than MCL on Consolidated3.19, but MCL-CAw performed considerably better than MCL on the "more noisy" Consolidated0.623.

Srihari et al. BMC Bioinformatics 2010 11:504   doi:10.1186/1471-2105-11-504

Open Data