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	GSfam	1.27e-01	1.96e-01	2.08e-01	2.56e-02
GSfam Exclusive	GeneGroup1	4.86e-03	9.69e-01	2.67e-02	7.59e-01
GeneGroup1 Exclusive	GSfam Exclusive	1.20e-01	8.03e-02	8.48e-02	3.24e-02
GSfam Exclusive	GeneGroup1 Exclusive	4.81e-03	9.81e-01	8.14e-03	9.48e-01
GeneGroup1 Exclusive	Overlap	9.83e-01	9.68e-01	8.01e-01	8.78e-02
GSfam Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	1.74e-06
Overlap	Exclusives	9.02e-04	3.61e-04	7.39e-14	1.60e-05



Evaluating how well GeneGroup1 genes are linked to GSfam 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	GSfam	0.64	-1.07	-2.07	-0.57	3.35
GSfam Exclusive	GeneGroup1	0.51	0.22	0.04	0.33	0.24
GeneGroup1 Exclusive	GSfam Exclusive	0.63	-1.17	-2.74	-0.92	2.78
GSfam Exclusive	GeneGroup1 Exclusive	0.50	-0.34	-0.33	-0.01	-0.18
GeneGroup1 Exclusive	Overlap	0.80	0.29	0.54	0.63	2.00
GSfam Exclusive	Overlap	1.00	2.50	2.82	2.57	2.91
Overlap	Exclusives	0.60	2.29	3.18	2.78	4.23

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	GSfam	0.00	-0.59	-1.67	-0.50	2.02
GSfam Exclusive	GeneGroup1	0.01	4.08	3.14	2.57	0.88
GeneGroup1 Exclusive	GSfam Exclusive	0.00	-0.69	-1.67	-0.53	2.05
GSfam Exclusive	GeneGroup1 Exclusive	0.01	-0.94	-0.85	-0.40	-0.72
GeneGroup1 Exclusive	Overlap	0.00	-0.11	0.06	0.03	0.62
GSfam Exclusive	Overlap	0.07	246.90	66.77	248.76	223.52
Overlap	Exclusives	0.03	12.58	32.98	12.72	19.32

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	118	118	
GSfam Exclusive	32	32	
Overlap	3	3