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Table 2 Gene set enrichment analysis of 394 ER-positive breast cancers: part 2

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
   LN- over LN+ Grade 3 over grade 1 Grade 3 over grade 2 Grade 2 over grade 1
  Gene set NES Nominal P FWER P NES Nominal P FWER P NES Nominal P FWER P NES Nominal P FWER P
Modulation of E2 and ER Estrogen/ER induced -1.38 0.07 0.47 1.40 0.07 0.45 1.14 0.27 0.78 1.27 0.15 0.63
  Estrogen/ER repressed 1.35 0.11 0.52 -1.51 0.05 0.28 -1.27 0.16 0.62 -1.21 0.18 0.69
Modulation of oxidative stress Ox induced 1.14 0.30 0.79 1.44 0.08 0.38 1.55 0.06 0.23 0.78 0.75 0.98
  Ox repressed 1.03 0.42 0.87 -1.32 0.11 0.57 -1.51 0.03 0.29 -0.88 0.65 0.95
  Ox-E/ER Ox induced 1.10 0.36 0.82 1.11 0.34 0.80 1.11 0.35 0.82 -0.98 0.46 0.90
  Ox-E/ER Ox repressed 1.24 0.20 0.69 -1.00 0.44 0.90 -1.34 0.12 0.54 -0.42 1.00 1.00
Modulation of ER and oxidative stress Ox' induced 1.00 0.44 0.89 1.50 0.05 0.30 1.53 0.06 0.25 0.82 0.70 0.97
  Ox' repressed 0.99 0.47 0.90 -1.74 0.01 0.06 -1.70 0.01 0.09 -1.19 0.21 0.73
  Ox'-E/ER Ox induced 1.03 0.42 0.87 0.91 0.52 0.93 0.75 0.77 0.98 -1.43 0.12 0.40
  Ox'-E/ER Ox repressed 1.24 0.20 0.68 -1.65 0.02 0.12 -1.35 0.13 0.53 -1.48 0.06 0.32
Literaturea MAPK induced 0.99 0.45 0.90 0.81 0.70 0.98 0.95 0.52 0.92 -0.55 0.96 1.00
  MAPK repressed -1.09 0.31 0.81 1.06 0.38 0.84 -1.02 0.44 0.88 1.17 0.27 0.75
  Luminal markers 1.19 0.32 0.73 -1.71 0.02 0.08 -1.77 0.01 0.05 -0.81 0.65 0.97
  Sustained estrogen-induced -1.20 0.23 0.69 1.79 0.00 0.03 1.33 0.11 0.54 1.63 0.02 0.14
  Proliferation markers -1.76 0.02 0.06 2.02 0.00 0.00 1.97 0.00 0.00 1.90 0.00 0.01
  1. Gene sets showing nominal enrichment (p < 0.05) are denoted in bold.
  2. 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; LN, lymph node; NES, normalized enrichment score; Ox-E/ER, oxidant-sensitive estrogen/ER gene signature; PR, progesterone receptor.