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)
All-Familial	AD-Final25	3.49e-02	6.67e-01	3.51e-01	1.10e-01
AD-Final25	All-Familial	1.28e-04	3.97e-01	4.76e-01	2.61e-04



Evaluating how well All-Familial genes are linked to AD-Final25 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)
All-Familial	AD-Final25	0.61	-1.02	-0.39	-0.09	2.06
AD-Final25	All-Familial	0.64	-1.34	-1.53	-1.18	3.92

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)
All-Familial	AD-Final25	0.00	-1.01	-0.85	-0.28	0.45
AD-Final25	All-Familial	0.00	-0.66	-1.72	-0.68	2.71

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	 
All-Familial	60	60	
AD-Final25	25	25