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Table 1 Molecular pathways and properties of their expression networks

From: Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules

ER-       
Pathway nG nE fE Pval(signif) fconsE Pval(consist)
MYC 76 472 0.17 < 0.001 0.88 < 0.001
E2F3 104 793 0.15 < 0.001 0.58 < 0.001
RAS 135 1387 0.15 < 0.001 0.63 < 0.001
ERBB2 228 4223 0.16 < 0.001 0.84 < 0.001
EGFR 180 2395 0.15 < 0.001 0.66 < 0.001
AKT 41 346 0.42 < 0.001 1.00 < 0.001
IL12 17 38 0.28 < 0.001 0.95 < 0.001
IL4 11 9 0.16 0.11 1.00 < 0.001
IL2 19 22 0.13 0.19 0.73 0.009
IL13 7 6 0.29 0.01 1.00 < 0.001
INFG 40 222 0.28 < 0.001 0.90 < 0.001
TGFB 62 479 0.25 < 0.001 0.92 < 0.001
ER+       
Pathway nG nE fE Pval(signif) fconsE Pval(consist)
MYC 76 749 0.26 0.24 0.79 < 0.001
E2F3 104 1285 0.24 0.58 0.57 < 0.001
RAS 135 2231 0.25 0.48 0.57 < 0.001
ERBB2 228 7336 0.28 0.01 0.74 < 0.001
EGFR 180 4286 0.27 0.13 0.66 < 0.001
AKT 41 676 0.82 < 0.001 1.00 < 0.001
IL12 17 32 0.23 0.53 0.97 < 0.001
IL4 11 10 0.18 0.72 0.70 0.06
IL2 19 40 0.23 0.51 0.60 0.08
IL13 7 6 0.29 0.28 0.50 0.35
INFG 40 284 0.36 0.003 0.83 < 0.001
TGFB 62 713 0.38 < 0.001 0.86 < 0.001
  1. Properties of the inferred relevance expression correlation networks in ER- and ER+ breast cancer. For each molecular pathway we give the number of pathway genes present in the expression matrix (nG), the number and fraction of edges (i.e significant pairwise correlations between genes) (nE & fE), the significance of the average connectivity of the network (Pval(signif)), the fraction of edges that are consistent with the prior in-vitro information (fconsE), the corresponding p-value of significance (Pval(consist)). P-values were estimated using 1000 permutations.