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Table 2 Summary of gene layer network for both datasets of breast cancer genes

From: Two-layer modular analysis of gene and protein networks in breast cancer

 

Set 1: West et al.[30]

Set 2: Gyorffy et al.[31]

 

All samples

ER+

ER-

ALL samples

HER2+

ER+/HER2

ER-/HER2-

Number of samples

49

25

24

1809

295

1285

229

Number of genes

610

610

610

796

796

796

796

λ

0.80

0.81

0.83

0.03

0.14

0.04

0.18

qval

0.30

0.30

0.30

0.30

0.30

0.30

0.30

Genes

513

464

459

796

791

789

793

Number of interactions

4619

5718

1960

3488

6086

2745

7546

α

1.23

1.37

1.38

1.35

1.25

1.40

1.21

Qmax

0.25

0.19

0.47

0.35

0.23

0.39

0.23

Number of modules

7

7

10

10

7

11

6

% accuracy, LOO-CV

78

71

60

57

61

76

72

Similarity measure

 

86

74

 

87

83

88

  1. λ, optimal shrinkage intensity; qval, cut off for the partial correlation (the threshold is adjusted so as to ensure that all well-studied breast cancer marker genes are included in the networks); α, power-law exponent; Qmax, maximum modularity score; LOO-CV, Leave-one-out cross-validation.
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BMC Systems Biology

ISSN: 1752-0509

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