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)
74_swap_AD Exclusive	GS_Tier1	5.72e-11	1.50e-10	1.82e-12	2.14e-12
GS_Tier1 Exclusive	74_swap_AD	6.24e-02	7.60e-02	2.96e-02	5.75e-03
74_swap_AD Exclusive	GS_Tier1 Exclusive	2.55e-08	2.23e-09	1.28e-09	2.58e-09
GS_Tier1 Exclusive	74_swap_AD Exclusive	3.22e-01	1.33e-01	3.00e-02	3.34e-02
74_swap_AD Exclusive	Overlap	5.60e-06	1.83e-06	9.14e-09	2.50e-06
GS_Tier1 Exclusive	Overlap	1.83e-09	1.83e-09	1.83e-09	1.83e-09
Overlap	Exclusives	3.07e-06	1.41e-05	8.70e-17	1.92e-06



Evaluating how well 74_swap_AD genes are linked to GS_Tier1 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)
74_swap_AD Exclusive	GS_Tier1	0.84	4.38	6.51	3.77	7.30
GS_Tier1 Exclusive	74_swap_AD	0.61	3.65	2.40	3.33	3.35
74_swap_AD Exclusive	GS_Tier1 Exclusive	0.82	4.01	6.38	3.98	5.58
GS_Tier1 Exclusive	74_swap_AD Exclusive	0.58	2.79	2.16	3.08	2.32
74_swap_AD Exclusive	Overlap	0.99	2.67	2.89	2.67	3.63
GS_Tier1 Exclusive	Overlap	1.00	3.07	3.14	2.90	2.94
Overlap	Exclusives	0.67	4.82	5.51	3.88	5.04

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)
74_swap_AD Exclusive	GS_Tier1	0.03	46.50	83.64	59.52	44.67
GS_Tier1 Exclusive	74_swap_AD	0.04	49.15	52.03	51.45	58.37
74_swap_AD Exclusive	GS_Tier1 Exclusive	0.02	46.67	91.63	43.53	36.86
GS_Tier1 Exclusive	74_swap_AD Exclusive	0.02	32.12	30.02	28.74	25.22
74_swap_AD Exclusive	Overlap	0.01	16.18	18.86	26.10	17.30
GS_Tier1 Exclusive	Overlap	0.10	342.00	121.45	208.56	191.76
Overlap	Exclusives	0.11	69.00	145.22	133.48	175.66

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	 
74_swap_AD Exclusive	70	69	RFPL2
GS_Tier1 Exclusive	27	26	MS4A
Overlap	4	4