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	GSgwas	5.93e-01	8.35e-01	6.00e-01	2.10e-04
GSgwas Exclusive	GeneGroup1	1.78e-01	9.84e-01	2.34e-05	6.82e-01
GeneGroup1 Exclusive	GSgwas Exclusive	6.84e-01	9.08e-01	6.68e-01	7.03e-05
GSgwas Exclusive	GeneGroup1 Exclusive	1.47e-01	9.05e-01	6.01e-05	7.92e-01
GeneGroup1 Exclusive	Overlap	4.99e-01	5.97e-01	3.58e-01	2.11e-01
GSgwas Exclusive	Overlap	4.01e-03	6.93e-03	6.57e-07	5.45e-05
Overlap	Exclusives	3.05e-02	1.55e-01	2.92e-24	9.20e-05



Evaluating how well GeneGroup1 genes are linked to GSgwas 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	GSgwas	0.63	-0.42	-0.35	-0.49	5.03
GSgwas Exclusive	GeneGroup1	0.51	1.09	0.12	1.12	1.01
GeneGroup1 Exclusive	GSgwas Exclusive	0.63	-0.42	-0.06	-0.33	4.73
GSgwas Exclusive	GeneGroup1 Exclusive	0.50	0.61	-0.22	0.47	0.14
GeneGroup1 Exclusive	Overlap	0.63	-0.74	-1.00	-0.90	1.04
GSgwas Exclusive	Overlap	0.93	3.45	3.62	3.91	3.93
Overlap	Exclusives	0.57	2.81	2.97	2.48	5.41

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	GSgwas	0.01	-0.25	0.75	-0.15	6.45
GSgwas Exclusive	GeneGroup1	0.02	4.84	3.35	2.65	3.27
GeneGroup1 Exclusive	GSgwas Exclusive	0.01	-0.11	1.05	-0.14	3.30
GSgwas Exclusive	GeneGroup1 Exclusive	0.02	0.30	-0.36	-0.12	-0.43
GeneGroup1 Exclusive	Overlap	0.00	-0.83	-0.95	-0.85	-0.12
GSgwas Exclusive	Overlap	0.11	297.42	303.98	308.60	110.05
Overlap	Exclusives	0.04	6.96	7.78	6.70	9.88

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	344	343	11-Sep
GSgwas Exclusive	149	126	LINC00675;LINC00603;SAT2B-AS1;POUF5F1B;CDKN2B-AS1;SNHG15;RTELI;HLA class II;SnoU13;ZMIZ1-AS1;LINC00917;45358;c11orf53;LINC00673;TERC;METRLN;LOC146513;ANRIL; MYNN;SCL22A3;HLA class I; PIGU;COLCA1
Overlap	8	8