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)
HPO-T2D Exclusive	CMDKP-T2D	8.12e-03	1.98e-02	5.22e-06	1.58e-05
CMDKP-T2D Exclusive	HPO-T2D	1.47e-03	2.53e-03	1.42e-06	3.86e-07
HPO-T2D Exclusive	CMDKP-T2D Exclusive	1.78e-01	7.60e-02	6.14e-04	1.69e-04
CMDKP-T2D Exclusive	HPO-T2D Exclusive	2.34e-02	2.89e-02	5.89e-05	5.63e-05
HPO-T2D Exclusive	Overlap	1.64e-08	1.51e-08	5.56e-09	1.78e-08
CMDKP-T2D Exclusive	Overlap	5.77e-07	2.30e-06	4.08e-07	6.47e-07
Overlap	Exclusives	8.46e-11	1.33e-10	8.35e-39	1.35e-19



Evaluating how well HPO-T2D genes are linked to CMDKP-T2D 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)
HPO-T2D Exclusive	CMDKP-T2D	0.62	2.65	3.59	2.83	4.90
CMDKP-T2D Exclusive	HPO-T2D	0.64	1.28	1.94	1.17	5.92
HPO-T2D Exclusive	CMDKP-T2D Exclusive	0.60	2.18	2.78	2.29	4.10
CMDKP-T2D Exclusive	HPO-T2D Exclusive	0.61	0.65	1.02	1.03	5.71
HPO-T2D Exclusive	Overlap	0.99	3.04	5.74	3.64	5.03
CMDKP-T2D Exclusive	Overlap	0.97	4.09	4.42	3.55	5.27
Overlap	Exclusives	0.69	7.11	8.20	3.90	12.08

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)
HPO-T2D Exclusive	CMDKP-T2D	0.02	4.33	9.60	6.66	9.47
CMDKP-T2D Exclusive	HPO-T2D	0.03	10.38	15.17	8.56	19.13
HPO-T2D Exclusive	CMDKP-T2D Exclusive	0.01	2.22	2.19	3.06	4.88
CMDKP-T2D Exclusive	HPO-T2D Exclusive	0.02	4.16	7.63	5.11	10.50
HPO-T2D Exclusive	Overlap	0.02	30.61	112.98	52.31	94.42
CMDKP-T2D Exclusive	Overlap	0.05	100.47	110.70	101.93	55.92
Overlap	Exclusives	0.06	39.55	33.03	27.39	46.16

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	 
HPO-T2D Exclusive	149	146	SNORD116-1;PWRN1;SNORD115-1
CMDKP-T2D Exclusive	146	141	CTC-236F12.4;AL627309.1;AC022431.2;AL117190.2;CTD-2021H9.3
Overlap	9	9