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	2.21e-01	1.57e-01	5.68e-02	4.02e-02
GWAS-identified	Hallmark	1.65e-02	1.84e-06	1.12e-06	1.54e-14



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	0.70	1.69	2.52	2.26	2.12
GWAS-identified	Hallmark	0.76	0.77	4.41	1.47	6.81

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	0.00	0.48	-0.47	3.14	0.91
GWAS-identified	Hallmark	0.01	0.31	0.30	1.21	4.49

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	59	59	
GWAS-identified	13	12	R73