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)
GeneGroup1 Exclusive	GeneGroup2	7.16e-02	4.00e-02	2.43e-13	3.85e-11
GeneGroup2 Exclusive	GeneGroup1	6.11e-02	2.06e-01	2.43e-15	6.09e-15
GeneGroup1 Exclusive	GeneGroup2 Exclusive	1.08e-01	5.00e-02	2.15e-13	1.64e-09
GeneGroup2 Exclusive	GeneGroup1 Exclusive	6.78e-02	2.56e-01	8.54e-15	3.27e-15
GeneGroup1 Exclusive	Overlap	7.71e-02	7.71e-02	7.71e-02	2.28e-02
GeneGroup2 Exclusive	Overlap	5.30e-01	2.16e-01	8.22e-02	6.71e-04
Overlap	Exclusives	2.95e-08	6.15e-06	3.91e-110	1.25e-25



Evaluating how well GeneGroup1 genes are linked to GeneGroup2 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)
GeneGroup1 Exclusive	GeneGroup2	0.63	-0.73	1.28	1.35	7.11
GeneGroup2 Exclusive	GeneGroup1	0.71	0.63	1.93	2.05	9.26
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.63	-0.40	1.32	1.39	5.81
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.71	0.66	1.68	2.55	9.98
GeneGroup1 Exclusive	Overlap	0.92	-0.36	1.04	1.44	2.54
GeneGroup2 Exclusive	Overlap	0.96	0.50	1.89	1.79	2.62
Overlap	Exclusives	0.70	5.08	5.87	2.10	11.41

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)
GeneGroup1 Exclusive	GeneGroup2	0.03	-0.39	9.00	7.00	29.21
GeneGroup2 Exclusive	GeneGroup1	0.04	1.13	8.52	5.46	26.78
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.02	-1.73	1.81	3.19	8.07
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.03	1.38	6.49	8.09	28.72
GeneGroup1 Exclusive	Overlap	0.28	1.33	336.20	37.92	229.86
GeneGroup2 Exclusive	Overlap	0.02	-0.53	62.70	3.43	104.63
Overlap	Exclusives	0.05	8.78	15.26	6.07	26.83

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	 
GeneGroup1 Exclusive	200	177	RTELI;SCL22A3;LINC00603; MYNN;ANRIL;HLA class I;CDKN2B-AS1;COLCA1;SNHG15;LINC00675; PIGU;SAT2B-AS1;HLA class II;METRLN;TERC;LINC00917;LINC00673;c11orf53;LOC146513;ZMIZ1-AS1;SnoU13;7-Mar;POUF5F1B
GeneGroup2 Exclusive	165	165	
Overlap	3	3