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	5.08e-03	3.46e-01	7.79e-20	5.23e-12
GeneGroup2	GeneGroup1	1.27e-01	1.48e-01	4.68e-03	3.30e-03



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	0.66	0.63	0.46	0.57	7.21
GeneGroup2	GeneGroup1	0.75	-1.17	0.11	0.47	2.69

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	0.02	1.56	1.83	2.29	7.05
GeneGroup2	GeneGroup1	0.01	3.83	16.39	6.17	6.30

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	11	11	
GeneGroup2	182	175	AC003002.1;NLGN4Y;AC100868.1;UGT2A1;CHD2;nan;USP9Y