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)
sigma209 Exclusive	GSfam	2.62e-01	1.84e-01	5.28e-01	1.01e-03
GSfam Exclusive	sigma209	1.39e-05	9.91e-01	2.19e-03	9.20e-01
sigma209 Exclusive	GSfam Exclusive	2.15e-01	1.19e-01	2.82e-01	1.70e-03
GSfam Exclusive	sigma209 Exclusive	2.14e-05	9.93e-01	9.67e-04	9.86e-01
sigma209 Exclusive	Overlap	6.03e-01	1.45e-01	6.40e-01	3.45e-02
GSfam Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	4.36e-06
Overlap	Exclusives	1.10e-02	1.15e-02	1.34e-18	7.61e-05



Evaluating how well sigma209 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)
sigma209 Exclusive	GSfam	0.69	-0.83	-2.03	-0.66	3.52
GSfam Exclusive	sigma209	0.51	-0.36	-0.19	0.24	0.52
sigma209 Exclusive	GSfam Exclusive	0.67	-1.01	-1.86	-0.80	3.88
GSfam Exclusive	sigma209 Exclusive	0.50	-0.62	-0.27	0.09	0.15
sigma209 Exclusive	Overlap	0.80	-0.25	-1.43	0.32	2.10
GSfam Exclusive	Overlap	1.00	2.71	3.06	2.64	2.67
Overlap	Exclusives	0.57	2.55	2.96	2.09	4.17

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)
sigma209 Exclusive	GSfam	0.00	-0.51	-1.85	-0.38	4.06
GSfam Exclusive	sigma209	0.01	0.79	1.10	1.31	1.25
sigma209 Exclusive	GSfam Exclusive	0.00	-0.77	-1.76	-0.50	3.77
GSfam Exclusive	sigma209 Exclusive	0.01	-0.93	-0.59	-0.38	-0.27
sigma209 Exclusive	Overlap	0.00	-0.53	-1.17	-0.17	0.67
GSfam Exclusive	Overlap	0.07	221.45	78.49	257.94	64.11
Overlap	Exclusives	0.03	10.31	20.40	12.14	16.97

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	 
sigma209 Exclusive	206	205	45546
GSfam Exclusive	32	32	
Overlap	3	3