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)
URGeneEmbed Exclusive	GS	5.48e-05	1.54e-03	1.63e-46	5.24e-26
GS Exclusive	URGeneEmbed	2.12e-09	1.97e-05	3.24e-42	4.27e-44
URGeneEmbed Exclusive	GS Exclusive	1.68e-03	4.26e-03	5.84e-41	8.61e-23
GS Exclusive	URGeneEmbed Exclusive	3.75e-06	3.31e-04	1.60e-35	3.41e-40
URGeneEmbed Exclusive	Overlap	2.81e-04	5.13e-03	2.79e-09	1.03e-07
GS Exclusive	Overlap	9.57e-12	1.76e-09	1.22e-17	7.12e-17
Overlap	Exclusives	8.53e-11	7.18e-12	1.21e-52	1.16e-56



Evaluating how well URGeneEmbed 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)
URGeneEmbed Exclusive	GS	0.77	3.00	5.10	5.06	12.12
GS Exclusive	URGeneEmbed	0.83	1.43	6.14	4.73	15.93
URGeneEmbed Exclusive	GS Exclusive	0.75	3.40	4.99	4.23	10.75
GS Exclusive	URGeneEmbed Exclusive	0.81	0.97	4.99	4.42	14.83
URGeneEmbed Exclusive	Overlap	0.95	1.94	2.60	3.00	5.43
GS Exclusive	Overlap	0.99	3.94	4.32	3.23	6.17
Overlap	Exclusives	0.78	3.60	10.14	4.64	18.56

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)
URGeneEmbed Exclusive	GS	0.06	3.36	14.36	18.78	62.52
GS Exclusive	URGeneEmbed	0.07	1.20	17.35	12.72	70.83
URGeneEmbed Exclusive	GS Exclusive	0.04	2.63	10.84	10.81	43.09
GS Exclusive	URGeneEmbed Exclusive	0.04	-1.91	5.42	5.79	41.32
URGeneEmbed Exclusive	Overlap	0.10	2.95	39.75	45.15	37.67
GS Exclusive	Overlap	0.20	5.82	253.72	154.75	491.59
Overlap	Exclusives	0.08	4.44	32.46	20.18	57.94

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	 
URGeneEmbed Exclusive	174	173	PES 1.00
GS Exclusive	191	168	LINC00917;ZMIZ1-AS1;HLA class I;SCL22A3;CDKN2B-AS1;COLCA1;HLA class II;METRLN;LINC00673; PIGU;RTELI;TERC;7-Mar;ANRIL;LINC00603;POUF5F1B; MYNN;LOC146513;SAT2B-AS1;SnoU13;c11orf53;LINC00675;SNHG15
Overlap	12	12