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	1.52e-05	1.17e-01	3.29e-05	1.64e-05
GeneGroup2 Exclusive	GeneGroup1	4.52e-03	2.94e-02	5.58e-05	5.91e-11
GeneGroup1 Exclusive	GeneGroup2 Exclusive	3.68e-05	1.33e-01	6.05e-05	2.47e-05
GeneGroup2 Exclusive	GeneGroup1 Exclusive	1.15e-02	6.23e-02	3.90e-04	5.97e-11
GeneGroup1 Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	9.92e-02
GeneGroup2 Exclusive	Overlap	1.49e-01	5.90e-01	9.92e-02	1.25e-01
Overlap	Exclusives	1.50e-15	5.41e-13	3.89e-50	2.01e-26



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	0.63	0.82	2.22	1.45	5.71
GeneGroup2 Exclusive	GeneGroup1	0.70	-0.31	1.97	0.93	7.42
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.63	1.08	1.93	1.53	6.10
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.70	-0.01	1.52	0.94	7.54
GeneGroup1 Exclusive	Overlap	1.00	1.43	3.19	1.62	1.65
GeneGroup2 Exclusive	Overlap	0.94	0.22	0.90	0.87	1.58
Overlap	Exclusives	0.74	1.44	8.38	2.20	11.89

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	-0.66	1.11	1.06	3.09
GeneGroup2 Exclusive	GeneGroup1	0.01	-0.84	0.78	0.37	3.79
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.01	-0.57	0.55	1.20	2.58
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.01	-0.64	0.62	0.31	7.38
GeneGroup1 Exclusive	Overlap	0.01	15.38	139.83	24.43	15.10
GeneGroup2 Exclusive	Overlap	0.00	-0.32	-0.16	0.28	1.31
Overlap	Exclusives	0.06	6.46	27.98	5.48	39.98

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	107	103	MBL3P;HLA-DRB4;SRY;SNORA31
GeneGroup2 Exclusive	147	147	
Overlap	1	1