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)
20_GeneEmbed_AD Exclusive	GS_tier1	6.52e-07	2.79e-08	1.04e-12	1.59e-10
GS_tier1 Exclusive	20_GeneEmbed_AD	7.97e-05	3.03e-05	1.95e-07	1.60e-09
20_GeneEmbed_AD Exclusive	GS_tier1 Exclusive	6.68e-07	4.71e-08	3.83e-12	8.15e-10
GS_tier1 Exclusive	20_GeneEmbed_AD Exclusive	3.09e-04	3.45e-05	1.51e-06	2.15e-08
20_GeneEmbed_AD Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	5.94e-02
GS_tier1 Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	1.98e-02
Overlap	Exclusives	2.03e-17	1.24e-15	2.46e-34	2.17e-23



Evaluating how well 20_GeneEmbed_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)
20_GeneEmbed_AD Exclusive	GS_tier1	0.83	4.05	5.89	3.16	6.07
GS_tier1 Exclusive	20_GeneEmbed_AD	0.88	2.25	5.18	2.42	5.63
20_GeneEmbed_AD Exclusive	GS_tier1 Exclusive	0.83	4.71	5.56	2.93	5.66
GS_tier1 Exclusive	20_GeneEmbed_AD Exclusive	0.88	2.27	4.75	2.23	5.45
20_GeneEmbed_AD Exclusive	Overlap	0.98	0.76	1.45	1.65	1.80
GS_tier1 Exclusive	Overlap	1.00	1.19	1.26	1.64	1.60
Overlap	Exclusives	0.91	2.82	8.37	2.42	10.35

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)
20_GeneEmbed_AD Exclusive	GS_tier1	0.01	3.50	10.38	3.18	14.44
GS_tier1 Exclusive	20_GeneEmbed_AD	0.01	5.86	18.42	8.58	18.10
20_GeneEmbed_AD Exclusive	GS_tier1 Exclusive	0.01	3.15	8.36	2.63	8.39
GS_tier1 Exclusive	20_GeneEmbed_AD Exclusive	0.01	3.69	13.46	4.68	9.42
20_GeneEmbed_AD Exclusive	Overlap	0.00	-0.12	9.21	1.51	0.17
GS_tier1 Exclusive	Overlap	0.02	34.69	32.92	26.39	62.27
Overlap	Exclusives	0.03	17.19	42.82	9.72	9.25

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	 
20_GeneEmbed_AD Exclusive	19	19	
GS_tier1 Exclusive	30	29	MS4A
Overlap	1	1