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)
magma Exclusive	gwas2	6.26e-01	9.15e-01	9.13e-01	3.41e-01
gwas2 Exclusive	magma	4.75e-01	5.32e-01	5.25e-01	1.64e-01
magma Exclusive	gwas2 Exclusive	3.53e-01	8.44e-01	8.63e-01	4.59e-01
gwas2 Exclusive	magma Exclusive	9.55e-01	5.97e-01	7.70e-01	2.69e-01
magma Exclusive	Overlap	8.84e-01	5.84e-01	8.14e-01	4.72e-01
gwas2 Exclusive	Overlap	1.38e-03	1.38e-03	1.45e-03	1.45e-03
Overlap	Exclusives	3.95e-08	1.13e-07	2.32e-16	6.61e-09



Evaluating how well magma genes are linked to gwas2 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)
magma Exclusive	gwas2	0.56	-0.49	0.56	-0.20	1.37
gwas2 Exclusive	magma	0.59	2.06	1.09	1.12	1.83
magma Exclusive	gwas2 Exclusive	0.55	-0.60	0.46	-0.16	0.74
gwas2 Exclusive	magma Exclusive	0.55	0.91	0.02	0.17	0.81
magma Exclusive	Overlap	0.66	-0.43	0.49	0.29	1.08
gwas2 Exclusive	Overlap	1.00	4.42	2.92	2.88	2.93
Overlap	Exclusives	0.75	7.19	7.49	4.28	6.27

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)
magma Exclusive	gwas2	0.00	-0.49	0.38	-0.20	0.34
gwas2 Exclusive	magma	0.01	11.19	12.88	6.55	13.41
magma Exclusive	gwas2 Exclusive	0.00	-0.63	0.08	-0.36	-0.11
gwas2 Exclusive	magma Exclusive	0.00	0.05	-0.53	-0.17	0.02
magma Exclusive	Overlap	0.00	-0.13	2.57	2.52	1.44
gwas2 Exclusive	Overlap	0.04	170.57	121.84	40.83	61.26
Overlap	Exclusives	0.02	34.32	26.09	10.44	41.21

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	 
magma Exclusive	28	26	MICA;KIAA1751
gwas2 Exclusive	36	35	HLA
Overlap	3	3