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_GoldStandard_Lambert	APOE_NegativeEpistasis	6.17e-01	6.63e-02	2.45e-02	1.34e-08
APOE_NegativeEpistasis	AD_GoldStandard_Lambert	6.75e-01	3.25e-01	6.83e-03	3.77e-03



Evaluating how well AD_GoldStandard_Lambert genes are linked to APOE_NegativeEpistasis 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_GoldStandard_Lambert	APOE_NegativeEpistasis	0.66	0.92	2.64	1.18	5.66
APOE_NegativeEpistasis	AD_GoldStandard_Lambert	0.67	1.52	1.89	1.09	3.50

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_GoldStandard_Lambert	APOE_NegativeEpistasis	0.01	0.42	0.83	1.05	4.38
APOE_NegativeEpistasis	AD_GoldStandard_Lambert	0.00	-0.25	0.32	0.12	0.97

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_GoldStandard_Lambert	31	30	MS4A
APOE_NegativeEpistasis	117	117