The method compares the distribution of the t-test statistic values per gene within a pathway with the distribution of the same statistic in the remaining genes using two z-score tests. These two tests are based on two different null hypothesis obtained through a permutation on samples and on genes. In the following table the significantly enriched pathways (NEk q-value and NTk q-value <= 0.05) are reported. Otherwise the top 50 pathways are shown.

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Pathway	Set Size	Percent Up	NTk Stat	NTk q-value	NTk Rank	NEk Stat	NEk q-value	NEk Rank
NF-kappa B signaling pathway	60.0	83.33	-7.55	0.0	1.0	-3.09	0.092	2.0
Measles	74.0	75.68	-6.47	0.0	3.0	-3.09	0.092	2.0
Osteoclast differentiation	95.0	78.95	-7.54	0.0	2.0	-2.51	0.208	7.5
Influenza A	81.0	72.84	-5.43	0.0	6.0	-2.88	0.138	4.0
Legionellosis	31.0	77.42	-4.98	0.0	7.0	-2.65	0.222	5.0
Apoptosis	71.0	74.65	-4.82	0.0	10.0	-3.09	0.092	2.0
Natural killer cell mediated cytotoxicity	78.0	66.67	-5.83	0.0	5.0	-2.46	0.194	9.5
Hepatitis B	97.0	68.04	-4.82	0.0	9.0	-2.51	0.208	7.5
Amoebiasis	36.0	80.56	-4.24	0.0	13.0	-2.58	0.231	6.0
Toll-like receptor signaling pathway	71.0	73.24	-4.95	0.0	8.0	-2.14	0.261	16.0
Rheumatoid arthritis	15.0	80.0	-3.86	0.0	15.0	-2.26	0.302	11.0
Herpes simplex infection	59.0	71.19	-4.22	0.0	14.0	-2.17	0.297	13.5
HIF-1 signaling pathway	87.0	64.37	-3.16	0.0	21.0	-2.46	0.194	9.5
Cytosolic DNA-sensing pathway	18.0	77.78	-3.37	0.0	20.0	-2.2	0.323	12.0
T cell receptor signaling pathway	77.0	64.94	-3.53	0.0	18.0	-2.14	0.261	16.0
Antigen processing and presentation	36.0	91.67	-6.45	0.0	4.0	-1.83	0.285	32.5
Chagas disease (American trypanosomiasis)	71.0	69.01	-3.52	0.0	19.0	-2.12	0.248	18.5
Intestinal immune network for IgA production	18.0	88.89	-4.55	0.0	12.0	-1.94	0.267	26.0
B cell receptor signaling pathway	57.0	68.42	-3.62	0.0	17.0	-1.96	0.288	24.0
Toxoplasmosis	74.0	71.62	-3.09	0.007	23.5	-2.12	0.248	18.5
Malaria	8.0	75.0	-3.09	0.007	23.5	-2.1	0.249	20.0
Epstein-Barr virus infection	67.0	62.69	-2.75	0.019	30.0	-2.17	0.297	13.5
Viral myocarditis	20.0	75.0	-2.88	0.013	28.0	-2.14	0.261	16.0
Jak-STAT signaling pathway	81.0	67.9	-3.09	0.007	23.5	-2.0	0.277	22.5
Leishmaniasis	37.0	75.68	-3.75	0.0	16.0	-1.81	0.277	34.5
Amino sugar and nucleotide sugar metabolism	38.0	81.58	-2.88	0.013	28.0	-2.0	0.277	22.5
Hepatitis C	66.0	65.15	-3.09	0.007	23.5	-1.9	0.268	29.5
Salmonella infection	46.0	73.91	-2.65	0.023	32.5	-1.94	0.267	26.0
African trypanosomiasis	13.0	76.92	-2.26	0.058	38.0	-2.05	0.264	21.0
Cell adhesion molecules (CAMs)	64.0	68.75	-4.67	0.0	11.0	-1.47	0.364	54.0
Selenocompound metabolism	8.0	37.5	2.23	0.059	40.5	1.94	0.267	26.0
NOD-like receptor signaling pathway	31.0	64.52	-2.26	0.058	38.0	-1.9	0.268	29.5
Pertussis	41.0	70.73	-2.65	0.023	32.5	-1.72	0.29	40.5
Serotonergic synapse	60.0	70.0	-2.26	0.058	38.0	-1.79	0.285	36.0
Cholinergic synapse	70.0	68.57	-1.96	0.1	47.0	-1.91	0.277	28.0
RIG-I-like receptor signaling pathway	33.0	69.7	-2.51	0.033	34.0	-1.59	0.31	49.5
Long-term depression	45.0	71.11	-2.12	0.076	42.0	-1.64	0.321	44.0
Dorso-ventral axis formation	10.0	70.0	-1.67	0.155	56.0	-1.84	0.295	31.0
Fat digestion and absorption	8.0	12.5	2.23	0.059	40.5	1.61	0.318	47.0
Transcriptional misregulation in cancer	15.0	80.0	-1.67	0.155	56.0	-1.83	0.285	32.5
Graft-versus-host disease	8.0	100.0	-2.92	0.007	26.0	-1.39	0.348	65.5
Steroid hormone biosynthesis	25.0	68.0	-1.74	0.145	53.0	-1.73	0.298	39.0
Leukocyte transendothelial migration	66.0	69.7	-2.88	0.013	28.0	-1.39	0.348	65.5
Retinol metabolism	26.0	65.38	-1.91	0.109	48.0	-1.63	0.313	45.5
Amyotrophic lateral sclerosis (ALS)	32.0	68.75	-1.77	0.14	51.0	-1.65	0.316	43.0
p53 signaling pathway	50.0	66.0	-2.01	0.092	45.0	-1.59	0.31	49.5
Long-term potentiation	55.0	61.82	-1.58	0.184	58.0	-1.77	0.284	37.0
Citrate cycle (TCA cycle)	23.0	43.48	2.75	0.018	31.0	1.36	0.349	68.0
Glutamatergic synapse	67.0	70.15	-2.07	0.083	43.0	-1.45	0.36	57.0
Vibrio cholerae infection	14.0	71.43	-1.33	0.247	69.0	-1.81	0.277	34.5