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)
APOE4_122 Exclusive	GS_31	2.19e-01	1.18e-01	8.58e-02	6.71e-02
GS_31 Exclusive	APOE4_122	8.51e-02	5.00e-01	2.91e-01	6.28e-01
APOE4_122 Exclusive	GS_31 Exclusive	4.08e-01	2.38e-01	2.97e-01	2.00e-01
GS_31 Exclusive	APOE4_122 Exclusive	7.57e-02	7.38e-01	4.96e-01	6.29e-01
APOE4_122 Exclusive	Overlap	1.92e-01	5.17e-01	1.21e-01	1.34e-02
GS_31 Exclusive	Overlap	9.85e-05	9.85e-05	9.85e-05	9.85e-05
Overlap	Exclusives	4.26e-05	1.91e-05	4.51e-15	1.04e-05



Evaluating how well APOE4_122 genes are linked to GS_31 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)
APOE4_122 Exclusive	GS_31	0.61	0.53	1.04	0.26	2.25
GS_31 Exclusive	APOE4_122	0.53	0.42	0.27	-0.16	1.28
APOE4_122 Exclusive	GS_31 Exclusive	0.59	0.16	0.41	-0.07	1.47
GS_31 Exclusive	APOE4_122 Exclusive	0.52	0.18	0.00	-0.10	1.04
APOE4_122 Exclusive	Overlap	0.96	2.04	1.91	1.82	2.40
GS_31 Exclusive	Overlap	1.00	2.40	1.92	2.22	2.20
Overlap	Exclusives	0.61	4.06	4.25	2.77	4.82

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)
APOE4_122 Exclusive	GS_31	0.00	0.46	1.71	0.97	0.20
GS_31 Exclusive	APOE4_122	0.01	1.20	1.76	1.87	3.47
APOE4_122 Exclusive	GS_31 Exclusive	0.00	0.19	0.79	0.42	0.57
GS_31 Exclusive	APOE4_122 Exclusive	0.01	0.39	0.42	0.13	1.16
APOE4_122 Exclusive	Overlap	0.00	0.69	13.94	2.82	4.41
GS_31 Exclusive	Overlap	0.05	145.26	106.75	246.07	123.60
Overlap	Exclusives	0.04	30.92	48.22	30.63	30.96

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	 
APOE4_122 Exclusive	120	120	
GS_31 Exclusive	29	28	MS4A
Overlap	2	2