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)
202AA Exclusive	211AllAPOE	2.10e-01	1.88e-01	9.73e-02	2.27e-02
211AllAPOE Exclusive	202AA	2.87e-01	4.01e-01	2.14e-01	2.87e-01
202AA Exclusive	211AllAPOE Exclusive	2.90e-01	1.72e-01	2.33e-01	1.92e-01
211AllAPOE Exclusive	202AA Exclusive	3.16e-01	5.23e-01	2.57e-01	3.01e-01
202AA Exclusive	Overlap	2.32e-01	7.53e-02	1.18e-01	2.57e-03
211AllAPOE Exclusive	Overlap	9.06e-01	8.18e-01	8.78e-01	1.12e-01
Overlap	Exclusives	8.03e-01	7.76e-01	1.82e-16	1.20e-01



Evaluating how well 202AA genes are linked to 211AllAPOE 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)
202AA Exclusive	211AllAPOE	0.55	1.81	2.03	1.76	2.52
211AllAPOE Exclusive	202AA	0.54	1.06	0.84	0.97	1.52
202AA Exclusive	211AllAPOE Exclusive	0.54	1.79	1.73	1.51	1.66
211AllAPOE Exclusive	202AA Exclusive	0.53	1.29	0.91	1.03	1.62
202AA Exclusive	Overlap	0.72	1.19	1.84	1.39	2.42
211AllAPOE Exclusive	Overlap	0.62	-0.28	-0.39	-0.37	1.59
Overlap	Exclusives	0.52	-0.49	0.16	0.31	1.48

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)
202AA Exclusive	211AllAPOE	0.01	1.50	2.56	1.38	3.27
211AllAPOE Exclusive	202AA	0.01	2.00	1.72	2.33	1.87
202AA Exclusive	211AllAPOE Exclusive	0.01	1.95	3.05	1.30	2.27
211AllAPOE Exclusive	202AA Exclusive	0.01	2.54	1.67	2.15	1.43
202AA Exclusive	Overlap	0.00	0.48	-3.01	0.35	1.63
211AllAPOE Exclusive	Overlap	0.00	0.05	0.03	0.28	0.85
Overlap	Exclusives	0.02	0.22	0.49	0.43	1.09

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	 
202AA Exclusive	188	188	
211AllAPOE Exclusive	197	196	RFPL2
Overlap	14	14