Comparing distributions of experimental and random diffusion values (p-values for KS tests)
Seeds	Recipients	Randomize Seeds (degree-matched)	Randomize Recipients (degree-matched)	Randomize Seeds (uniform)	Randomize Recipients (uniform)
Regulome_selected_2_AD_79_74 Exclusive	TIER1_GS	5.07e-09	1.68e-09	3.15e-08	1.99e-13
TIER1_GS Exclusive	Regulome_selected_2_AD_79_74	6.38e-02	7.27e-02	1.65e-02	5.65e-02
Regulome_selected_2_AD_79_74 Exclusive	TIER1_GS Exclusive	2.17e-09	6.79e-10	2.58e-08	4.58e-12
TIER1_GS Exclusive	Regulome_selected_2_AD_79_74 Exclusive	1.16e-01	1.17e-01	4.83e-02	9.89e-02
Regulome_selected_2_AD_79_74 Exclusive	Overlap	5.17e-01	5.17e-01	5.17e-01	2.24e-01
TIER1_GS Exclusive	Overlap	9.85e-05	9.85e-05	9.85e-05	2.96e-04
Overlap	Exclusives	1.86e-04	6.20e-06	2.61e-17	3.08e-06



Evaluating how well Regulome_selected_2_AD_79_74 genes are linked to TIER1_GS genes, comparing against random

ROC results
Seeds	Recipients	AUROC	Z-score for Random Seeds (degree-matched)	Z-score for Random Recipients (degree-matched)	Z-score for Random Seeds (uniform)	Z-score for Random Recipients (uniform)
Regulome_selected_2_AD_79_74 Exclusive	TIER1_GS	0.87	4.13	6.89	3.90	7.42
TIER1_GS Exclusive	Regulome_selected_2_AD_79_74	0.57	3.06	2.44	2.29	2.33
Regulome_selected_2_AD_79_74 Exclusive	TIER1_GS Exclusive	0.88	4.92	7.99	3.79	6.77
TIER1_GS Exclusive	Regulome_selected_2_AD_79_74 Exclusive	0.56	2.43	2.23	2.28	1.92
Regulome_selected_2_AD_79_74 Exclusive	Overlap	0.83	1.27	1.29	1.23	1.73
TIER1_GS Exclusive	Overlap	1.00	2.79	1.99	2.41	2.60
Overlap	Exclusives	0.66	3.56	5.98	2.38	5.51

PRC results
Seeds	Recipients	AUPRC	Z-score for Random Seeds (degree-matched)	Z-score for Random Recipients (degree-matched)	Z-score for Random Seeds (uniform)	Z-score for Random Recipients (uniform)
Regulome_selected_2_AD_79_74 Exclusive	TIER1_GS	0.01	8.64	22.09	6.79	20.87
TIER1_GS Exclusive	Regulome_selected_2_AD_79_74	0.01	4.14	15.87	11.49	11.23
Regulome_selected_2_AD_79_74 Exclusive	TIER1_GS Exclusive	0.01	11.04	14.60	8.18	12.61
TIER1_GS Exclusive	Regulome_selected_2_AD_79_74 Exclusive	0.01	4.71	9.08	3.02	2.97
Regulome_selected_2_AD_79_74 Exclusive	Overlap	0.00	9.18	33.20	12.15	9.93
TIER1_GS Exclusive	Overlap	0.02	33.49	51.07	57.32	32.01
Overlap	Exclusives	0.02	19.63	28.22	11.64	22.82

Z-scores are computed for the experimental area under ROC or PRC based on distributions of the random areas under these curves
Seeds: Genes where diffusion signal starts FROM)
Recipients: Genes that receive the diffusion signal and that are in the other validated group
Random genes are selected either uniformly or degree matched



Number of genes
**	#Total	# Mapped in the network	Not mapped genes	 
Regulome_selected_2_AD_79_74 Exclusive	72	68	PRAMEF15;AC005779.2;AL451062.3;TMEM191C
TIER1_GS Exclusive	29	28	MS4A
Overlap	2	2