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_199 Exclusive	tier1_31	4.77e-03	5.72e-03	1.37e-03	1.75e-05
tier1_31 Exclusive	Regulome_selected_2_AD_79_199	3.55e-01	2.32e-01	1.35e-01	6.35e-02
Regulome_selected_2_AD_79_199 Exclusive	tier1_31 Exclusive	7.70e-03	1.59e-02	9.69e-03	6.44e-05
tier1_31 Exclusive	Regulome_selected_2_AD_79_199 Exclusive	6.26e-01	3.33e-01	4.02e-01	8.53e-02
Regulome_selected_2_AD_79_199 Exclusive	Overlap	2.03e-02	8.07e-02	2.50e-03	8.38e-05
tier1_31 Exclusive	Overlap	9.39e-10	5.59e-06	4.47e-11	4.61e-08
Overlap	Exclusives	3.42e-04	4.50e-04	5.03e-18	4.32e-04



Evaluating how well Regulome_selected_2_AD_79_199 genes are linked to tier1_31 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_199 Exclusive	tier1_31	0.77	3.04	4.76	2.75	5.21
tier1_31 Exclusive	Regulome_selected_2_AD_79_199	0.55	1.49	1.31	1.66	2.33
Regulome_selected_2_AD_79_199 Exclusive	tier1_31 Exclusive	0.74	2.48	3.39	2.20	4.53
tier1_31 Exclusive	Regulome_selected_2_AD_79_199 Exclusive	0.54	0.99	1.13	1.05	2.12
Regulome_selected_2_AD_79_199 Exclusive	Overlap	0.93	2.39	2.61	2.52	3.16
tier1_31 Exclusive	Overlap	0.99	3.20	3.23	3.37	4.17
Overlap	Exclusives	0.59	3.98	4.07	2.95	4.37

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_199 Exclusive	tier1_31	0.01	4.98	8.87	4.00	10.25
tier1_31 Exclusive	Regulome_selected_2_AD_79_199	0.02	7.21	6.51	7.12	5.68
Regulome_selected_2_AD_79_199 Exclusive	tier1_31 Exclusive	0.00	2.54	5.74	2.22	1.87
tier1_31 Exclusive	Regulome_selected_2_AD_79_199 Exclusive	0.01	1.11	2.34	2.23	1.87
Regulome_selected_2_AD_79_199 Exclusive	Overlap	0.00	5.84	6.79	8.34	15.39
tier1_31 Exclusive	Overlap	0.04	134.61	50.97	202.98	61.58
Overlap	Exclusives	0.06	53.21	59.97	47.77	43.28

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_199 Exclusive	194	183	AC005779.2;TAF11L13;FAM205C;AL451062.3;OOSP3;HNRNPA1P48;AC010197.2;TMEM191C;AC106886.5;CCDC187;PRAMEF15
tier1_31 Exclusive	26	25	MS4A
Overlap	5	5