|  | 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 |