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_AD_WESr2_randomly_selection_z35 Exclusive	tier1_31	2.87e-01	3.72e-01	3.77e-01	1.89e-02
tier1_31 Exclusive	APOE3_AD_WESr2_randomly_selection_z35	7.98e-01	9.77e-02	1.34e-01	5.94e-02
APOE3_AD_WESr2_randomly_selection_z35 Exclusive	tier1_31 Exclusive	3.26e-01	7.26e-01	3.56e-01	1.95e-02
tier1_31 Exclusive	APOE3_AD_WESr2_randomly_selection_z35 Exclusive	7.67e-01	2.74e-01	8.28e-02	1.24e-01
APOE3_AD_WESr2_randomly_selection_z35 Exclusive	Overlap	2.57e-01	4.16e-01	6.93e-01	5.35e-01
tier1_31 Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	1.98e-02
Overlap	Exclusives	3.12e-08	9.84e-08	6.74e-09	1.10e-08



Evaluating how well APOE3_AD_WESr2_randomly_selection_z35 genes are linked to tier1_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_AD_WESr2_randomly_selection_z35 Exclusive	tier1_31	0.63	0.97	0.95	0.47	2.62
tier1_31 Exclusive	APOE3_AD_WESr2_randomly_selection_z35	0.57	0.90	1.59	1.23	1.72
APOE3_AD_WESr2_randomly_selection_z35 Exclusive	tier1_31 Exclusive	0.63	1.15	0.68	0.60	2.15
tier1_31 Exclusive	APOE3_AD_WESr2_randomly_selection_z35 Exclusive	0.56	0.93	1.03	1.69	1.53
APOE3_AD_WESr2_randomly_selection_z35 Exclusive	Overlap	0.74	1.23	0.88	0.59	0.80
tier1_31 Exclusive	Overlap	1.00	1.68	2.00	1.91	1.62
Overlap	Exclusives	0.68	2.27	5.30	2.63	5.07

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_AD_WESr2_randomly_selection_z35 Exclusive	tier1_31	0.00	0.17	-0.25	-0.17	0.81
tier1_31 Exclusive	APOE3_AD_WESr2_randomly_selection_z35	0.00	1.66	2.45	0.60	2.36
APOE3_AD_WESr2_randomly_selection_z35 Exclusive	tier1_31 Exclusive	0.00	0.38	-0.35	-0.06	0.37
tier1_31 Exclusive	APOE3_AD_WESr2_randomly_selection_z35 Exclusive	0.00	0.14	0.50	0.45	0.49
APOE3_AD_WESr2_randomly_selection_z35 Exclusive	Overlap	0.00	0.26	-0.10	-0.21	-0.12
tier1_31 Exclusive	Overlap	0.06	55.87	403.25	77.54	14.26
Overlap	Exclusives	0.04	9.12	44.82	20.95	47.52

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_AD_WESr2_randomly_selection_z35 Exclusive	67	65	AC093155.3;RFPL2
tier1_31 Exclusive	30	29	MS4A
Overlap	1	1