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)
GroupA	GroupB	1.86e-05	7.12e-10	6.09e-13	2.74e-17
GroupB	GroupA	1.35e-04	4.89e-03	8.48e-05	1.24e-03



Evaluating how well GroupA genes are linked to GroupB 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)
GroupA	GroupB	0.75	1.38	6.47	1.76	10.21
GroupB	GroupA	0.91	3.77	2.41	2.59	2.71

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)
GroupA	GroupB	0.02	1.89	6.83	2.40	8.39
GroupB	GroupA	0.00	12.80	2.74	5.71	1.36

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	 
GroupA	4	4	
GroupB	110	109	CHD2