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)
APOE3_analysis_positive	APOE3_ analysis_negative	4.49e-01	8.09e-01	7.71e-01	5.96e-01
APOE3_ analysis_negative	APOE3_analysis_positive	9.43e-01	7.16e-01	9.17e-01	8.66e-01



Evaluating how well APOE3_analysis_positive genes are linked to APOE3_ analysis_negative 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)
APOE3_analysis_positive	APOE3_ analysis_negative	0.52	-0.88	-0.56	-0.40	0.73
APOE3_ analysis_negative	APOE3_analysis_positive	0.51	-0.82	-1.05	-0.56	0.46

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)
APOE3_analysis_positive	APOE3_ analysis_negative	0.01	-0.94	-0.87	-0.90	-0.14
APOE3_ analysis_negative	APOE3_analysis_positive	0.00	-0.30	-1.14	-0.70	-0.30

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	 
APOE3_analysis_positive	49	49	
APOE3_ analysis_negative	107	105	AC093155.3;RFPL2