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)
gene_list Exclusive	GS	2.83e-01	2.61e-01	4.30e-05	2.49e-06
GS Exclusive	gene_list	6.64e-03	5.78e-01	1.06e-05	1.41e-15
gene_list Exclusive	GS Exclusive	1.20e-01	2.07e-01	9.56e-06	2.86e-06
GS Exclusive	gene_list Exclusive	3.60e-03	7.69e-01	3.16e-07	9.71e-16
gene_list Exclusive	Overlap	5.53e-01	7.40e-01	4.64e-01	4.05e-01
GS Exclusive	Overlap	1.15e-02	1.15e-02	1.15e-02	1.22e-02
Overlap	Exclusives	3.45e-01	2.46e-01	2.99e-20	1.04e-13



Evaluating how well gene_list genes are linked to 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)
gene_list Exclusive	GS	0.79	1.05	1.71	1.13	4.34
GS Exclusive	gene_list	0.66	0.59	0.85	0.74	8.09
gene_list Exclusive	GS Exclusive	0.80	1.31	2.05	1.57	4.13
GS Exclusive	gene_list Exclusive	0.66	0.37	0.74	0.66	7.81
gene_list Exclusive	Overlap	0.69	-0.77	-0.47	-0.26	0.82
GS Exclusive	Overlap	1.00	1.88	2.38	2.45	2.50
Overlap	Exclusives	0.66	-0.61	0.88	0.18	9.39

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)
gene_list Exclusive	GS	0.00	0.08	1.18	0.66	3.62
GS Exclusive	gene_list	0.02	2.26	1.60	3.37	8.28
gene_list Exclusive	GS Exclusive	0.00	0.19	1.49	1.08	5.69
GS Exclusive	gene_list Exclusive	0.02	0.97	0.68	2.52	7.17
gene_list Exclusive	Overlap	0.00	-0.84	-0.75	-0.33	-0.12
GS Exclusive	Overlap	0.04	42.71	148.02	130.65	7.64
Overlap	Exclusives	0.03	4.13	10.78	4.39	18.99

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	 
gene_list Exclusive	224	223	7-Sep
GS Exclusive	18	18	
Overlap	2	2