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_AC1 Exclusive	All-Familial	1.46e-04	1.93e-04	1.24e-09	5.83e-15
All-Familial Exclusive	vep_2method_RareCon_AC1	1.06e-02	6.40e-02	2.24e-06	2.71e-04
vep_2method_RareCon_AC1 Exclusive	All-Familial Exclusive	5.68e-03	1.02e-03	7.93e-07	2.77e-11
All-Familial Exclusive	vep_2method_RareCon_AC1 Exclusive	9.03e-03	4.20e-01	2.88e-04	4.54e-03
vep_2method_RareCon_AC1 Exclusive	Overlap	6.24e-03	5.35e-03	1.56e-04	3.08e-06
All-Familial Exclusive	Overlap	4.18e-08	4.37e-08	4.18e-08	4.77e-08
Overlap	Exclusives	4.44e-08	9.35e-08	2.46e-14	6.12e-12



Evaluating how well vep_2method_RareCon_AC1 genes are linked to All-Familial 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_AC1 Exclusive	All-Familial	0.84	2.57	5.38	2.46	8.86
All-Familial Exclusive	vep_2method_RareCon_AC1	0.62	1.81	2.28	2.27	4.81
vep_2method_RareCon_AC1 Exclusive	All-Familial Exclusive	0.83	2.46	4.15	2.58	7.76
All-Familial Exclusive	vep_2method_RareCon_AC1 Exclusive	0.59	1.56	1.32	1.43	3.71
vep_2method_RareCon_AC1 Exclusive	Overlap	0.96	2.14	3.18	2.03	4.31
All-Familial Exclusive	Overlap	1.00	2.62	4.34	2.48	4.64
Overlap	Exclusives	0.69	3.19	5.48	2.90	7.58

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_AC1 Exclusive	All-Familial	0.02	2.44	9.94	3.40	29.14
All-Familial Exclusive	vep_2method_RareCon_AC1	0.03	19.46	16.58	20.17	21.02
vep_2method_RareCon_AC1 Exclusive	All-Familial Exclusive	0.01	1.67	5.66	3.31	21.23
All-Familial Exclusive	vep_2method_RareCon_AC1 Exclusive	0.01	3.62	1.62	3.25	2.99
vep_2method_RareCon_AC1 Exclusive	Overlap	0.01	3.40	13.85	5.58	14.43
All-Familial Exclusive	Overlap	0.16	10.75	253.12	113.07	597.11
Overlap	Exclusives	0.04	17.17	27.57	20.86	26.55

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_AC1 Exclusive	118	117	PRAMEF11
All-Familial Exclusive	52	52	
Overlap	8	8