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	4.49e-01	8.04e-01	8.10e-01	3.39e-02
GeneGroup2	GeneGroup1	2.25e-01	7.44e-01	4.26e-01	9.31e-01



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	0.64	0.66	0.78	0.19	2.58
GeneGroup2	GeneGroup1	0.50	-0.29	0.04	-0.05	-0.01

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)
GeneGroup1	GeneGroup2	0.00	0.06	0.33	-0.19	0.75
GeneGroup2	GeneGroup1	0.00	-0.12	-0.16	0.04	-0.07

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	50	50	
GeneGroup2	25	25