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)
GeneGroup1	GeneGroup2	5.15e-20	1.80e-19	1.62e-19	9.67e-19
GeneGroup2	GeneGroup1	1.94e-05	1.94e-05	2.10e-05	2.10e-05



Evaluating how well GeneGroup1 genes are linked to GeneGroup2 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)
GeneGroup1	GeneGroup2	0.99	13.87	9.25	3.80	7.51
GeneGroup2	GeneGroup1	1.00	3.14	7.20	3.34	3.82

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)
GeneGroup1	GeneGroup2	0.13	858.64	181.61	40.59	295.52
GeneGroup2	GeneGroup1	0.07	146.72	518.43	218.07	342.50

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	 
GeneGroup1	5	5	
GeneGroup2	23	22	HLADRB1