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	1.08e-04	7.54e-04	1.16e-09	6.93e-08
GWAS-identified	Hallmark	6.66e-04	6.66e-04	7.45e-12	9.39e-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	6.52	66.36	2.78	4.53
GWAS-identified	Hallmark	1.00	10.12	3.96	3.16	3.72

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	0.04	586.23	451.93	56.92	24.55
GWAS-identified	Hallmark	0.04	1106.26	289.08	84.12	65.35

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	7	6	b4012