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	1.11e-01	3.04e-01	5.05e-06	1.95e-06
GS Exclusive	gene_list	4.53e-04	4.39e-01	3.90e-08	1.87e-22
gene_list Exclusive	GS Exclusive	8.07e-02	2.29e-01	2.21e-06	2.89e-06
GS Exclusive	gene_list Exclusive	7.05e-04	4.92e-01	1.91e-07	1.12e-22
gene_list Exclusive	Overlap	8.47e-01	6.52e-01	9.92e-02	1.85e-01
GS Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	9.92e-02
Overlap	Exclusives	3.22e-02	5.35e-02	8.58e-45	1.47e-26



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	0.80	1.58	2.23	1.63	4.79
GS Exclusive	gene_list	0.67	0.87	1.97	1.32	10.62
gene_list Exclusive	GS Exclusive	0.80	1.82	2.12	1.81	4.26
GS Exclusive	gene_list Exclusive	0.67	0.64	1.57	0.95	10.83
gene_list Exclusive	Overlap	0.88	0.12	0.15	0.83	1.29
GS Exclusive	Overlap	1.00	1.58	2.07	1.91	1.65
Overlap	Exclusives	0.69	0.80	2.73	1.32	11.13

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	0.95	2.33	1.45	2.85
GS Exclusive	gene_list	0.02	1.30	2.31	3.26	11.43
gene_list Exclusive	GS Exclusive	0.00	1.12	2.60	2.15	4.02
GS Exclusive	gene_list Exclusive	0.02	0.92	1.37	2.31	9.18
gene_list Exclusive	Overlap	0.00	-0.21	-0.47	0.17	0.40
GS Exclusive	Overlap	0.02	40.53	50.99	69.98	119.57
Overlap	Exclusives	0.03	2.92	6.01	2.83	17.44

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	290	289	7-Sep
GS Exclusive	19	19	
Overlap	1	1