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)
100_EPI_AD Exclusive	GS_tier1	1.79e-02	6.78e-02	1.29e-03	1.16e-04
GS_tier1 Exclusive	100_EPI_AD	1.17e-03	4.46e-05	1.73e-06	3.20e-09
100_EPI_AD Exclusive	GS_tier1 Exclusive	3.78e-02	4.78e-02	8.23e-03	1.13e-03
GS_tier1 Exclusive	100_EPI_AD Exclusive	4.21e-03	9.26e-05	4.44e-06	2.17e-08
100_EPI_AD Exclusive	Overlap	2.52e-01	5.17e-01	5.53e-02	4.89e-02
GS_tier1 Exclusive	Overlap	9.85e-05	9.85e-05	9.85e-05	9.85e-05
Overlap	Exclusives	1.88e-04	4.98e-09	2.27e-46	8.41e-19



Evaluating how well 100_EPI_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)
100_EPI_AD Exclusive	GS_tier1	0.71	1.87	2.54	1.84	4.56
GS_tier1 Exclusive	100_EPI_AD	0.72	2.60	5.86	2.67	7.59
100_EPI_AD Exclusive	GS_tier1 Exclusive	0.70	2.26	2.75	1.72	3.58
GS_tier1 Exclusive	100_EPI_AD Exclusive	0.71	2.38	6.21	3.18	7.47
100_EPI_AD Exclusive	Overlap	0.94	1.30	2.09	1.48	1.95
GS_tier1 Exclusive	Overlap	1.00	2.42	2.64	2.46	2.74
Overlap	Exclusives	0.77	5.30	10.09	2.32	10.25

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)
100_EPI_AD Exclusive	GS_tier1	0.01	11.42	5.68	10.90	8.66
GS_tier1 Exclusive	100_EPI_AD	0.01	2.62	9.23	5.19	4.60
100_EPI_AD Exclusive	GS_tier1 Exclusive	0.01	12.56	8.38	8.43	12.36
GS_tier1 Exclusive	100_EPI_AD Exclusive	0.01	2.34	7.62	4.26	9.12
100_EPI_AD Exclusive	Overlap	0.01	5.67	28.40	23.34	8.32
GS_tier1 Exclusive	Overlap	0.04	94.78	166.57	139.18	128.90
Overlap	Exclusives	0.08	109.22	104.97	28.05	124.42

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	 
100_EPI_AD Exclusive	98	98	
GS_tier1 Exclusive	29	28	MS4A
Overlap	2	2