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Table 12 cluster quality with and without false positives

From: The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks

Dataset

Number of Edges Removed

Edges Removed %

GO per Cluster

GO per Node

Depth of GO per Node

Number of Clusters with no significant annotation

Lehner

57

14%

19.2

1.2

5.8

1

Lehner plus False Positive Edges (FPE)

57

12.2%

18.2

1.1

5.7

1

Lehner (FPE edges removed)

57+68*

26.9%

19.33

1.3

5.7

10

Lehner random edges removed**

57+68*

26.9%

17.5 ± 4.6

1.3 ± 0.4

5.7 ± 0.08

4.2 ± 5.2

Ito minus FPE

57+26*

1.9%

1.3

0.1

4.7

149

Ito minus 26 random edges

57+26*

1.9%

1.3

0.1

4.7

146

  1. * edges removed for clustering + false positive or random edges removed
  2. **Lehner plus FPE with 68 edges removed at random (for 100 replicates mean ± standard deviation)
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BMC Bioinformatics

ISSN: 1471-2105

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