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_156 Exclusive	GS_31	2.99e-01	2.23e-01	4.07e-01	5.20e-02
GS_31 Exclusive	APOE3_156	2.46e-02	4.27e-01	3.32e-01	2.06e-01
APOE3_156 Exclusive	GS_31 Exclusive	3.78e-01	2.91e-01	6.73e-01	6.33e-02
GS_31 Exclusive	APOE3_156 Exclusive	2.41e-02	4.27e-01	4.53e-01	2.25e-01
APOE3_156 Exclusive	Overlap	7.52e-01	8.32e-01	7.13e-01	9.31e-01
GS_31 Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	1.98e-02
Overlap	Exclusives	2.54e-05	8.72e-04	3.13e-06	5.75e-05



Evaluating how well APOE3_156 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)
APOE3_156 Exclusive	GS_31	0.60	-0.12	-0.11	0.10	2.00
GS_31 Exclusive	APOE3_156	0.53	-0.68	-0.17	0.04	1.61
APOE3_156 Exclusive	GS_31 Exclusive	0.60	-0.07	0.01	-0.09	2.04
GS_31 Exclusive	APOE3_156 Exclusive	0.53	-0.43	-0.42	-0.21	1.14
APOE3_156 Exclusive	Overlap	0.60	-0.32	0.16	0.26	0.10
GS_31 Exclusive	Overlap	1.00	1.70	1.90	2.02	1.88
Overlap	Exclusives	0.60	2.24	3.28	2.45	4.66

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_156 Exclusive	GS_31	0.00	-0.36	-0.76	-0.15	0.25
GS_31 Exclusive	APOE3_156	0.01	0.71	0.87	1.23	1.15
APOE3_156 Exclusive	GS_31 Exclusive	0.00	-0.33	-0.59	-0.17	0.12
GS_31 Exclusive	APOE3_156 Exclusive	0.01	-0.09	-0.14	-0.11	0.49
APOE3_156 Exclusive	Overlap	0.00	-0.38	-0.23	-0.27	-0.32
GS_31 Exclusive	Overlap	0.06	97.99	74.46	349.68	143.50
Overlap	Exclusives	0.03	7.93	21.94	15.51	19.19

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_156 Exclusive	155	153	AC093155.3;RFPL2
GS_31 Exclusive	30	29	MS4A
Overlap	1	1