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	2.18e-26	1.55e-24	6.33e-27	3.00e-24
GWAS-identified	Hallmark	7.45e-12	7.45e-12	7.45e-12	1.57e-10



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	11.79	10.31	3.24	7.85
GWAS-identified	Hallmark	1.00	3.09	6.65	2.81	3.60

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	498.19	165.02	76.89	251.20
GWAS-identified	Hallmark	0.07	186.34	356.55	170.79	41.88

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