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)
Hallmark Exclusive	GWAS-identified	1.09e-27	7.90e-25	2.67e-27	1.69e-25
GWAS-identified Exclusive	Hallmark	1.18e-16	1.18e-16	1.18e-16	1.18e-16
Hallmark Exclusive	GWAS-identified Exclusive	2.62e-24	2.17e-22	1.31e-24	2.17e-22
GWAS-identified Exclusive	Hallmark Exclusive	7.45e-12	7.45e-12	7.45e-12	4.47e-11
Hallmark Exclusive	Overlap	9.85e-05	9.85e-05	9.85e-05	5.91e-04
GWAS-identified Exclusive	Overlap	9.85e-05	9.85e-05	9.85e-05	2.96e-04
Overlap	Exclusives	2.73e-33	2.77e-35	4.38e-32	6.01e-38



Evaluating how well Hallmark genes are linked to GWAS-identified 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)
Hallmark Exclusive	GWAS-identified	0.99	14.49	9.03	3.79	8.43
GWAS-identified Exclusive	Hallmark	1.00	4.44	6.90	3.66	4.38
Hallmark Exclusive	GWAS-identified Exclusive	0.98	14.06	8.96	3.17	7.77
GWAS-identified Exclusive	Hallmark Exclusive	1.00	2.81	6.34	3.06	3.88
Hallmark Exclusive	Overlap	1.00	10.82	3.59	3.58	2.40
GWAS-identified Exclusive	Overlap	1.00	3.32	3.69	3.29	2.31
Overlap	Exclusives	1.00	3.48	8.62	2.94	8.96

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)
Hallmark Exclusive	GWAS-identified	0.12	649.72	224.78	61.79	320.94
GWAS-identified Exclusive	Hallmark	0.29	546.48	1166.37	574.99	1110.04
Hallmark Exclusive	GWAS-identified Exclusive	0.10	525.83	160.21	42.24	75.54
GWAS-identified Exclusive	Hallmark Exclusive	0.07	85.86	278.60	188.85	55.76
Hallmark Exclusive	Overlap	0.04	4064.99	305.90	442.81	2.71
GWAS-identified Exclusive	Overlap	0.66	531.96	10458.07	5780.84	53.18
Overlap	Exclusives	0.34	296.63	644.29	34.99	1094.17

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	 
Hallmark Exclusive	5	5	
GWAS-identified Exclusive	21	21	
Overlap	2	2