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	8.24e-02	8.32e-02	7.53e-03	1.05e-06
GeneGroup2	GeneGroup1	6.16e-01	9.13e-01	8.14e-01	8.23e-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	0.79	0.63	2.12	0.87	5.62
GeneGroup2	GeneGroup1	0.66	-0.06	0.36	0.51	0.81

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)
GeneGroup1	GeneGroup2	0.00	0.17	3.81	1.27	4.17
GeneGroup2	GeneGroup1	0.00	0.72	0.04	1.84	0.41

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	3	3	
GeneGroup2	29	29