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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.