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)
96Swap AD Exclusive	GS_tier1	2.13e-08	4.01e-08	4.57e-09	1.09e-09
GS_tier1 Exclusive	96Swap AD	1.28e-01	2.56e-01	9.69e-02	7.89e-02
96Swap AD Exclusive	GS_tier1 Exclusive	1.08e-05	4.27e-07	3.35e-07	5.42e-07
GS_tier1 Exclusive	96Swap AD Exclusive	5.22e-01	4.94e-01	2.23e-01	1.14e-01
96Swap AD Exclusive	Overlap	8.32e-04	1.14e-02	5.01e-05	7.09e-06
GS_tier1 Exclusive	Overlap	1.83e-09	1.83e-09	1.83e-09	1.83e-09
Overlap	Exclusives	3.94e-05	1.53e-04	7.29e-14	4.69e-05



Evaluating how well 96Swap 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)
96Swap AD Exclusive	GS_tier1	0.82	3.70	5.78	3.31	5.77
GS_tier1 Exclusive	96Swap AD	0.58	3.64	2.10	2.25	2.55
96Swap AD Exclusive	GS_tier1 Exclusive	0.80	2.78	6.68	3.85	5.99
GS_tier1 Exclusive	96Swap AD Exclusive	0.56	2.67	1.33	1.96	2.15
96Swap AD Exclusive	Overlap	0.97	2.16	2.87	2.96	3.00
GS_tier1 Exclusive	Overlap	1.00	3.14	3.48	2.94	3.38
Overlap	Exclusives	0.63	4.23	5.59	3.48	4.41

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)
96Swap AD Exclusive	GS_tier1	0.01	10.32	30.91	8.60	7.98
GS_tier1 Exclusive	96Swap AD	0.03	48.37	39.69	24.49	37.67
96Swap AD Exclusive	GS_tier1 Exclusive	0.01	4.25	31.41	11.95	5.75
GS_tier1 Exclusive	96Swap AD Exclusive	0.02	21.20	21.93	8.32	21.27
96Swap AD Exclusive	Overlap	0.00	2.73	8.88	8.31	7.37
GS_tier1 Exclusive	Overlap	0.10	284.88	161.19	315.06	358.23
Overlap	Exclusives	0.09	50.19	147.95	82.26	128.35

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	 
96Swap AD Exclusive	92	91	RFPL2
GS_tier1 Exclusive	27	26	MS4A
Overlap	4	4