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

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

		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
Literature^a	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

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.

ISSN: 1465-542X