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)
Top 2 method genes Exclusive	Familial GS	3.40e-12	3.95e-11	7.36e-17	7.01e-20
Familial GS Exclusive	Top 2 method genes	3.17e-04	4.50e-03	2.16e-08	2.44e-04
Top 2 method genes Exclusive	Familial GS Exclusive	3.97e-09	3.77e-09	2.84e-13	5.42e-17
Familial GS Exclusive	Top 2 method genes Exclusive	6.31e-03	5.98e-02	1.22e-06	2.69e-03
Top 2 method genes Exclusive	Overlap	1.69e-04	1.77e-04	1.69e-04	2.81e-04
Familial GS Exclusive	Overlap	1.69e-04	1.69e-04	1.69e-04	1.77e-04
Overlap	Exclusives	1.53e-10	1.97e-08	1.53e-13	2.47e-13



Evaluating how well Top 2 method genes genes are linked to Familial GS 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)
Top 2 method genes Exclusive	Familial GS	0.95	3.20	8.33	2.88	9.06
Familial GS Exclusive	Top 2 method genes	0.65	2.64	2.02	2.52	4.18
Top 2 method genes Exclusive	Familial GS Exclusive	0.95	2.55	6.61	2.85	8.14
Familial GS Exclusive	Top 2 method genes Exclusive	0.63	2.58	1.83	1.86	4.00
Top 2 method genes Exclusive	Overlap	0.99	2.71	2.38	2.04	3.39
Familial GS Exclusive	Overlap	1.00	1.88	3.63	2.62	3.67
Overlap	Exclusives	0.72	1.94	3.32	1.85	6.35

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)
Top 2 method genes Exclusive	Familial GS	0.05	9.66	49.94	23.68	58.01
Familial GS Exclusive	Top 2 method genes	0.06	12.21	95.04	81.81	84.38
Top 2 method genes Exclusive	Familial GS Exclusive	0.04	6.10	37.08	12.39	33.07
Familial GS Exclusive	Top 2 method genes Exclusive	0.02	6.84	24.15	15.20	29.65
Top 2 method genes Exclusive	Overlap	0.01	16.03	20.87	19.32	12.39
Familial GS Exclusive	Overlap	0.33	144.93	1181.33	1063.28	305.52
Overlap	Exclusives	0.05	26.71	48.28	22.13	31.02

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	 
Top 2 method genes Exclusive	63	63	
Familial GS Exclusive	27	27	
Overlap	4	4