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)
AD Proxy Exclusive	GS1	4.93e-11	2.71e-11	4.83e-13	4.48e-12
GS1 Exclusive	AD Proxy	3.01e-01	4.93e-03	1.66e-02	9.14e-05
AD Proxy Exclusive	GS1 Exclusive	1.74e-10	1.07e-09	1.93e-11	4.86e-10
GS1 Exclusive	AD Proxy Exclusive	4.08e-01	1.01e-02	1.74e-02	2.95e-04
AD Proxy Exclusive	Overlap	9.09e-03	8.41e-03	9.82e-03	1.99e-03
GS1 Exclusive	Overlap	9.14e-09	3.84e-07	1.83e-09	3.84e-07
Overlap	Exclusives	1.61e-05	8.47e-05	1.38e-15	9.21e-06



Evaluating how well AD Proxy genes are linked to GS1 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)
AD Proxy Exclusive	GS1	0.87	5.95	7.12	4.87	7.27
GS1 Exclusive	AD Proxy	0.61	1.93	2.84	2.94	3.78
AD Proxy Exclusive	GS1 Exclusive	0.85	5.51	6.08	4.16	6.92
GS1 Exclusive	AD Proxy Exclusive	0.59	1.37	2.41	1.93	2.83
AD Proxy Exclusive	Overlap	0.95	2.42	2.74	2.16	3.55
GS1 Exclusive	Overlap	1.00	2.76	3.10	2.85	3.03
Overlap	Exclusives	0.66	4.31	5.89	3.43	5.75

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)
AD Proxy Exclusive	GS1	0.08	126.68	211.79	134.58	82.25
GS1 Exclusive	AD Proxy	0.04	21.84	72.19	68.41	81.38
AD Proxy Exclusive	GS1 Exclusive	0.06	147.62	185.94	82.92	182.40
GS1 Exclusive	AD Proxy Exclusive	0.03	15.78	55.85	18.03	42.80
AD Proxy Exclusive	Overlap	0.02	25.14	91.49	20.66	101.67
GS1 Exclusive	Overlap	0.08	118.80	108.80	191.02	135.24
Overlap	Exclusives	0.10	123.92	148.25	76.08	149.01

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	 
AD Proxy Exclusive	91	88	KDM5D;SERPINA3;TMEM265
GS1 Exclusive	27	26	MS4A
Overlap	4	4