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	GSfam	6.99e-02	1.99e-01	1.97e-04	3.00e-07
GSfam	GeneGroup1	4.99e-01	7.42e-02	7.41e-03	5.30e-03



Evaluating how well GeneGroup1 genes are linked to GSfam 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	GSfam	0.79	1.03	2.75	1.54	6.29
GSfam	GeneGroup1	0.66	2.45	2.15	2.54	3.32

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	GSfam	0.01	1.12	6.01	2.46	1.50
GSfam	GeneGroup1	0.00	0.55	2.11	2.00	2.62

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	36	36	
GSfam	35	35