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	GWAS-identified	4.76e-27	2.37e-23	1.11e-26	7.90e-25
GWAS-identified	Hallmark	7.45e-12	7.45e-12	7.45e-12	4.47e-11



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	GWAS-identified	0.99	12.20	9.46	3.35	8.12
GWAS-identified	Hallmark	1.00	2.64	6.80	3.14	4.02

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	GWAS-identified	0.12	539.23	136.33	79.69	345.58
GWAS-identified	Hallmark	0.07	132.81	305.87	215.65	114.33

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	5	5	
GWAS-identified	23	23