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	1.26e-01	1.77e-01	6.04e-01	6.29e-08
GeneGroup2 Exclusive	GeneGroup1	1.54e-02	7.08e-01	7.81e-03	5.02e-02
GeneGroup1 Exclusive	GeneGroup2 Exclusive	2.59e-01	1.41e-01	2.58e-01	9.97e-08
GeneGroup2 Exclusive	GeneGroup1 Exclusive	2.04e-02	7.55e-01	8.08e-03	7.07e-02
GeneGroup1 Exclusive	Overlap	4.00e-01	3.20e-01	1.85e-01	3.06e-01
GeneGroup2 Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	9.92e-02
Overlap	Exclusives	8.53e-04	1.86e-03	1.28e-11	7.13e-05



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	0.79	1.09	1.65	0.34	5.90
GeneGroup2 Exclusive	GeneGroup1	0.44	0.19	-0.50	-0.96	-1.93
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.79	0.71	2.08	-0.02	6.70
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.44	0.41	-0.55	-0.78	-1.93
GeneGroup1 Exclusive	Overlap	0.73	-0.59	-0.80	-1.36	0.95
GeneGroup2 Exclusive	Overlap	1.00	0.98	1.68	1.66	1.65
Overlap	Exclusives	0.57	0.92	0.80	0.66	2.55

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	0.00	0.99	0.80	-0.26	3.56
GeneGroup2 Exclusive	GeneGroup1	0.00	1.28	2.61	0.25	-0.18
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.00	0.58	1.11	-0.41	6.85
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.00	0.11	1.05	-0.16	-0.35
GeneGroup1 Exclusive	Overlap	0.00	-0.61	-1.30	-0.76	-0.09
GeneGroup2 Exclusive	Overlap	0.01	0.55	64.08	32.22	40.27
Overlap	Exclusives	0.02	13.88	16.54	6.36	9.43

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	79	77	C11orf97;UGT2A1
GeneGroup2 Exclusive	30	30	
Overlap	1	1