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)
2MethodControls	JLC	8.59e-02	2.84e-01	4.58e-01	6.00e-01
JLC	2MethodControls	8.68e-03	4.93e-01	1.80e-01	1.89e-01



Evaluating how well 2MethodControls genes are linked to JLC 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)
2MethodControls	JLC	0.56	-1.12	-1.75	-0.78	0.77
JLC	2MethodControls	0.53	-1.41	-1.59	-0.70	0.61

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)
2MethodControls	JLC	0.00	-0.56	-0.78	-0.58	-0.15
JLC	2MethodControls	0.00	-0.64	-0.23	-0.32	-0.10

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	 
2MethodControls	37	35	RMDN1;CSNK2A3
JLC	13	10	TRIF;UNC93B;NEMO