Table 2.

Sample data subjected to permutation analysis or comparison by gene symbol instead of probe ID

	10% Data permutation (10,891 trials)					Comparison by gene symbol
Name of L2L database list	Binomial p value (actual)	Median permutation binomial p value	p value (list-specific) of actual binomial p value	p value (all lists) of actual binomial p value	FDR of actual binomial p value	Total gene symbols on list	Expected matches	Actual matches	Binomial p value
ifn_beta_up	1.9E-14	4.7E-12	0.10	3.2E-03	0.58	93	4.46	25	1.3E-12
ifn_alpha_up	2.7E-14	1.4E-12	0.11	3.5E-03	0.31	71	3.41	22	1.2E-12
ifn_all_up	2.0E-10	1.1E-08	0.20	0.011	0.80	48	2.30	14	3.5E-08
nf90_up	3.1E-10	2.7E-09	0.21	0.012	0.70	37	1.78	11	8.3E-07
ifnalpha_both_up	1.6E-09	2.0E-08	0.28	0.014	0.70	21	1.01	8	3.3E-06
adip_diff_cluster2	1.8E-07	1.5E-06	0.32	0.019	0.86	30	1.44	9	7.7E-06
emt_up	5.1E-07	2.4E-06	0.25	0.021	0.84	68	3.26	11	3.8E-04
hpv31_dn	1.3E-06	7.2E-06	0.30	0.022	0.79	49	2.35	9	4.8E-04
ifnalpha_either_up	2.5E-06	1.2E-05	0.30	0.025	0.83	50	2.40	9	5.6E-04
adip_vs_fibro_up	3.2E-06	2.0E-05	0.34	0.027	0.79	35	1.68	4	0.085
hypoxia_normal_up	8.3E-06	6.3E-05	0.24	0.030	0.77	168	8.06	23	6.5E-06
hypoxia_reg	8.5E-06	4.7E-05	0.35	0.031	0.74	39	1.87	9	7.7E-05
tnfalpha_adip_up	5.3E-05	5.3E-05	0.54	0.048	0.75	8	0.38	1	0.33
cmv_up	1.0E-04	4.1E-04	0.37	0.056	0.74	59	2.83	11	1.0E-04
vhl_normal_up	1.8E-04	4.6E-04	0.31	0.065	0.78	155	7.44	19	1.8E-04
dsrna_up	1.9E-04	9.7E-04	0.45	0.068	0.75	33	1.58	8	1.3E-04
tnfalpha_tgz_adip_up	3.5E-04	3.5E-04	0.54	0.079	0.78	11	0.53	1	0.42
tgz_adip_up	7.1E-04	7.1E-04	0.55	0.093	0.77	14	0.67	1	0.50
hif1_targets	1.0E-03	4.2E-03	0.46	0.10	0.80	34	1.63	6	5.2E-03
adip_vs_preadip_up	1.9E-03	7.6E-03	0.49	0.12	0.80	35	1.68	3	0.24
serum_fibroblast_core_dn	5.1E-03	0.012	0.42	0.16	0.87	114	5.47	9	0.098
hypoxia_fibro_up	7.5E-03	7.5E-03	0.62	0.17	0.86	22	1.06	3	0.086