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	4.63e-03	1.07e-02	4.90e-01	4.67e-07
GeneGroup2 Exclusive	GeneGroup1	2.90e-02	5.66e-01	3.16e-01	2.12e-01
GeneGroup1 Exclusive	GeneGroup2 Exclusive	3.74e-03	1.24e-02	2.65e-01	3.72e-07
GeneGroup2 Exclusive	GeneGroup1 Exclusive	2.46e-02	7.60e-01	3.80e-01	1.83e-01
GeneGroup1 Exclusive	Overlap	4.91e-01	4.72e-01	1.85e-01	4.35e-01
GeneGroup2 Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	9.92e-02
Overlap	Exclusives	2.79e-07	1.56e-05	9.84e-22	1.27e-08



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	0.73	1.33	2.20	0.72	5.66
GeneGroup2 Exclusive	GeneGroup1	0.46	0.31	0.04	-0.72	-1.24
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.73	1.45	2.55	0.89	5.92
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.45	0.12	0.01	-0.58	-1.63
GeneGroup1 Exclusive	Overlap	0.73	-0.38	-0.54	-1.10	0.69
GeneGroup2 Exclusive	Overlap	1.00	0.87	1.56	1.53	1.57
Overlap	Exclusives	0.62	1.72	3.48	1.69	4.99

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	1.99	3.34	0.44	7.63
GeneGroup2 Exclusive	GeneGroup1	0.00	0.37	4.12	0.94	0.15
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.01	2.36	3.25	1.01	7.10
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.00	0.70	2.26	0.47	-0.06
GeneGroup1 Exclusive	Overlap	0.00	-0.49	-1.03	-0.38	-0.19
GeneGroup2 Exclusive	Overlap	0.01	0.40	48.84	10.13	18.31
Overlap	Exclusives	0.03	15.94	23.36	6.72	30.73

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	57	57	
Overlap	1	1