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	3.26e-02	1.80e-02	8.23e-03	4.55e-04
GeneGroup2 Exclusive	GeneGroup1	5.18e-12	4.93e-02	2.00e-01	3.84e-02
GeneGroup1 Exclusive	GeneGroup2 Exclusive	2.36e-02	2.01e-02	2.41e-03	1.10e-03
GeneGroup2 Exclusive	GeneGroup1 Exclusive	2.55e-12	3.40e-02	3.14e-01	1.55e-02
GeneGroup1 Exclusive	Overlap	7.12e-01	9.85e-01	9.13e-01	1.83e-01
GeneGroup2 Exclusive	Overlap	1.38e-03	1.38e-03	1.38e-03	1.38e-03
Overlap	Exclusives	2.91e-06	1.26e-05	5.85e-09	9.97e-07



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	-1.27	-3.60	-1.30	2.91
GeneGroup2 Exclusive	GeneGroup1	0.46	-2.98	-2.49	-2.13	-1.58
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.62	-1.45	-3.27	-1.62	2.55
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.45	-3.65	-2.53	-2.90	-2.32
GeneGroup1 Exclusive	Overlap	0.70	0.64	0.20	0.43	1.22
GeneGroup2 Exclusive	Overlap	1.00	3.39	3.34	2.87	3.39
Overlap	Exclusives	0.59	2.65	2.68	2.01	4.96

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	-1.44	-3.22	-1.46	0.63
GeneGroup2 Exclusive	GeneGroup1	0.02	16.80	12.91	10.57	9.40
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.00	-1.34	-3.19	-1.25	0.46
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.01	-2.52	-1.75	-1.38	-1.91
GeneGroup1 Exclusive	Overlap	0.00	-0.11	-0.34	-0.22	-0.06
GeneGroup2 Exclusive	Overlap	0.44	2712.85	2956.04	1806.47	955.14
Overlap	Exclusives	0.05	43.54	35.70	31.34	51.53

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	172	169	C17orf66;UBE2NL;LSMD1
GeneGroup2 Exclusive	52	52	
Overlap	3	3