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 Exclusive	GeneGroup2	6.00e-01	5.58e-01	7.31e-01	2.59e-04
GeneGroup2 Exclusive	GeneGroup1	1.74e-01	4.38e-01	1.26e-02	1.68e-01
GeneGroup1 Exclusive	GeneGroup2 Exclusive	7.83e-01	3.62e-01	6.07e-01	1.05e-03
GeneGroup2 Exclusive	GeneGroup1 Exclusive	1.30e-01	5.87e-01	1.16e-02	9.53e-02
GeneGroup1 Exclusive	Overlap	2.75e-01	5.14e-01	2.66e-01	3.41e-01
GeneGroup2 Exclusive	Overlap	5.27e-02	1.54e-01	1.73e-02	3.37e-02
Overlap	Exclusives	3.26e-02	8.35e-02	4.24e-12	7.70e-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 Exclusive	GeneGroup2	0.65	0.86	0.57	0.34	4.16
GeneGroup2 Exclusive	GeneGroup1	0.48	0.68	1.09	0.08	-1.02
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.65	0.51	0.60	0.11	3.92
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.47	0.42	0.83	-0.01	-1.33
GeneGroup1 Exclusive	Overlap	0.60	0.48	-0.03	-0.05	0.45
GeneGroup2 Exclusive	Overlap	0.93	2.12	1.71	2.41	2.25
Overlap	Exclusives	0.55	1.47	3.19	0.98	2.39

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 Exclusive	GeneGroup2	0.01	0.67	-0.46	-0.50	3.52
GeneGroup2 Exclusive	GeneGroup1	0.01	1.20	0.29	-0.04	-0.69
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.01	0.37	-0.07	-0.69	4.69
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.01	0.12	0.04	-0.45	-1.23
GeneGroup1 Exclusive	Overlap	0.00	0.05	-0.21	-0.28	-0.25
GeneGroup2 Exclusive	Overlap	0.01	61.58	35.53	28.02	25.80
Overlap	Exclusives	0.02	2.86	3.29	2.21	5.77

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 Exclusive	179	179	
GeneGroup2 Exclusive	66	62	OPTN ;MYOCOS;C12ORF23;SIX1 
Overlap	2	2