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	1.31e-18	4.91e-18	1.21e-18	5.11e-18
GWAS-identified	Hallmark	2.10e-05	2.10e-05	2.10e-05	2.10e-05



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	13.60	9.62	3.24	7.47
GWAS-identified	Hallmark	1.00	2.98	6.25	2.74	4.01

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	603.99	165.80	72.89	96.92
GWAS-identified	Hallmark	0.07	159.76	276.44	33.76	282.08

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