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)
vep_2method_RareCon_AC5 Exclusive	AD-Final25	2.05e-01	2.46e-01	3.07e-02	8.42e-03
AD-Final25 Exclusive	vep_2method_RareCon_AC5	2.16e-01	4.03e-01	2.01e-02	2.64e-04
vep_2method_RareCon_AC5 Exclusive	AD-Final25 Exclusive	4.93e-01	4.09e-01	8.87e-02	1.32e-02
AD-Final25 Exclusive	vep_2method_RareCon_AC5 Exclusive	1.95e-01	4.64e-01	2.33e-02	4.33e-04
vep_2method_RareCon_AC5 Exclusive	Overlap	9.92e-02	1.05e-01	9.92e-02	9.92e-02
AD-Final25 Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	9.92e-02
Overlap	Exclusives	1.70e-08	1.33e-08	3.37e-11	1.73e-11



Evaluating how well vep_2method_RareCon_AC5 genes are linked to AD-Final25 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)
vep_2method_RareCon_AC5 Exclusive	AD-Final25	0.70	0.55	2.01	1.08	3.47
AD-Final25 Exclusive	vep_2method_RareCon_AC5	0.58	0.97	1.24	0.96	4.63
vep_2method_RareCon_AC5 Exclusive	AD-Final25 Exclusive	0.69	0.22	1.38	0.72	3.26
AD-Final25 Exclusive	vep_2method_RareCon_AC5 Exclusive	0.58	0.89	0.99	0.91	4.02
vep_2method_RareCon_AC5 Exclusive	Overlap	0.98	2.19	2.26	2.17	1.74
AD-Final25 Exclusive	Overlap	1.00	2.12	2.22	2.17	1.71
Overlap	Exclusives	0.64	2.46	4.78	2.00	7.11

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)
vep_2method_RareCon_AC5 Exclusive	AD-Final25	0.00	0.25	0.20	0.83	1.14
AD-Final25 Exclusive	vep_2method_RareCon_AC5	0.01	1.46	2.03	2.12	5.25
vep_2method_RareCon_AC5 Exclusive	AD-Final25 Exclusive	0.00	-0.20	-0.19	0.24	1.31
AD-Final25 Exclusive	vep_2method_RareCon_AC5 Exclusive	0.01	0.98	0.98	1.47	2.83
vep_2method_RareCon_AC5 Exclusive	Overlap	0.00	20.83	7.21	0.96	6.78
AD-Final25 Exclusive	Overlap	0.12	886.50	1880.90	415.07	509.22
Overlap	Exclusives	0.04	13.39	24.62	13.21	30.06

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	 
vep_2method_RareCon_AC5 Exclusive	196	194	;PRAMEF11
AD-Final25 Exclusive	24	24	
Overlap	1	1