Table 2.

Gene sets/pathways enrichment in phenotypes MMTV and CTRL. Rows shaded in gray show the significantly enriched pathways in both MMTV and CTRL phenotypes. ES: Enrichment Score, NES: Normalized Enrichment Score, NOM: Nominal, FDR: False Discovery Rate, FWER: Family-wise Error Rate.

Gene Sets	Size	ES	NES	NOM p-Value	FDR q-Value	FWER p-Value
Gene sets enriched in MMTV phenotype.
TNF	110	0.34	1.37	0.222	0.215	0.170
Autophagy	137	0.24	1.37	0.000	0.159	0.170
Type II interferon	65	0.54	1.37	0.233	0.133	0.170
P53	70	0.23	1.25	0.000	0.169	0.451
Notch	57	0.24	1.23	0.240	0.164	0.570
Apoptosis	142	0.22	1.21	0.000	0.169	0.650
Cell cycle	121	0.23	1.13	0.245	0.284	0.950
NFƙB	97	0.31	1.08	0.422	0.325	0.950
ErBb	85	0.20	0.94	0.442	0.525	0.950
Gene sets enriched in CTRL phenotype.
WNT	140	−0.35	−1.83	0.000	0.030	0.000
Hedgehog	79	−0.38	−1.76	0.000	0.053	0.070
Focal adhesion	195	−0.37	−1.63	0.000	0.045	0.100
Rap1	205	−0.35	−1.59	0.000	0.067	0.140
Metabolism	130	−0.66	−1.58	0.000	0.068	0.140
PI3−AKT−mTOR	395	−0.29	−1.56	0.000	0.080	0.140
Prolactin	76	−0.38	−1.54	0.000	0.076	0.140
EGFR	38	−0.69	−1.52	0.000	0.072	0.140
PI3−AKT	310	−0.30	−1.52	0.000	0.069	0.140
Hippo	148	−0.27	−1.51	0.000	0.073	0.140
Ras	221	−0.30	−1.49	0.000	0.070	0.140
Inflammation	46	−0.37	−1.49	0.000	0.071	0.140
Glutathione	46	−0.55	−1.45	0.000	0.075	0.180
VEGF	74	−0.36	−1.43	0.000	0.073	0.180
cAMP	190	−0.33	−1.39	0.000	0.086	0.350
Immune response	95	−0.47	−1.39	0.000	0.083	0.350
Estrogen	119	−0.34	−1.38	0.000	0.079	0.350
Calcium	219	−0.34	−1.32	0.000	0.097	0.450
AMPK	88	−0.22	−1.30	0.054	0.104	0.480
PPAR	70	−0.34	−1.27	0.000	0.107	0.480
mTOR	140	−0.19	−1.25	0.000	0.115	0.520
Chemokine	166	−0.24	−1.22	0.364	0.154	0.670
HIF−1	68	−0.19	−1.20	0.239	0.169	0.670
MAPK	300	−0.22	−1.20	0.000	0.164	0.670
FoXo	93	−0.23	−1.19	0.255	0.165	0.710
Insulin	130	−0.22	−1.07	0.352	0.339	0.930
TGFB	102	−0.23	−1.06	0.412	0.372	1.000
JAK−STAT	147	−0.26	−1.03	0.352	0.429	1.000
Cytokines	201	−0.25	−1.01	0.528	0.430	1.000