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Table 1 Gene set enrichment analysis of 394 ER-positive breast cancers: part 1

From: Genes responsive to both oxidant stress and loss of estrogen receptor function identify a poor prognosis group of estrogen receptor positive primary breast cancers

   Comparison
   PR- over PR+ ERBB2- over ERBB2+ Age
  Gene set NES Nominal P FWER P NES Nominal P FWER P NES Nominal P FWER P
Modulation of E2 and ER Estrogen/ER induced -1.03 0.42 0.91 1.06 0.36 0.87 -1.60 0.02 0.18
  Estrogen/ER repressed -1.14 0.27 0.81 -0.99 0.46 0.90 1.67 0.01 0.11
Modulation of oxidative stress Ox induced 1.15 0.28 0.78 -1.61 0.04 0.19 -1.45 0.07 0.36
  Ox repressed -1.53 0.02 0.24 1.19 0.20 0.75 1.18 0.21 0.74
  Ox-E/ER Ox-induced 0.90 0.54 0.95 -1.43 0.11 0.40 -1.45 0.09 0.37
  Ox-E/ER Ox repressed -1.75 0.00 0.07 1.36 0.11 0.53 -1.13 0.29 0.81
Modulation of ER and oxidative stress Ox' induced 1.17 0.24 0.75 -1.66 0.02 0.13 -1.21 0.19 0.71
  Ox' repressed -1.54 0.04 0.23 1.21 0.21 0.73 1.71 0.01 0.09
  Ox'-E/ER Ox induced -1.30 0.15 0.61 -1.04 0.40 0.86 -1.19 0.24 0.75
  Ox'-E/ER Ox repressed -1.39 0.11 0.44 0.94 0.54 0.93 1.49 0.07 0.32
Literaturea MAPK induced 1.16 0.28 0.77 -0.98 0.48 0.91 -0.74 0.78 0.98
  MAPK repressed -1.17 0.25 0.77 1.09 0.33 0.83 0.99 0.46 0.92
  Luminal markers -1.69 0.03 0.10 1.68 0.02 0.11 1.85 0.00 0.01
  Sustained estrogen-induced 1.00 0.45 0.90 -1.26 0.18 0.64 -1.07 0.36 0.85
  Proliferation markers 1.92 0.00 0.01 -1.95 0.00 0.01 -1.70 0.04 0.09
  1. Gene sets showing nominal enrichment (P < 0.05) are denoted in bold. aMitogen-activated protein kinase (MAPK) [42], luminal [54], sustained estrogen-induced [43], and proliferation signatures [53] as shown in Additional file 2. E2, estradiol; ER, estrogen receptor; FWER, family-wise error rate; NES, normalized enrichment score; Ox-E/ER, oxidant-sensitive estrogen/ER gene signature; PR, progesterone receptor.