Parameter	Superior value	Inferior value	Number of unequal comparisons	Number of times superior value has higher accuracy	Number of times inferior value has higher accuracy	Number of times both values have equal accuracy	Mean accuracy of superior value	Mean accuracy of inferior value	Difference between mean accuracies	Paired Wilcoxon signed rank test p value	Level of significance
Results for all organisms merged											
Compound weight	Degree	Unit	52	52	0	0	0.79	0.65	0.14	1.80E-10	**
RPAIR class filtering	main-trans	main	32	25	7	0	0.74	0.72	0.02	8.85E-05	**
Graph type	RPAIR graph	Reaction-specific RPAIR graph	40	33	7	8	0.74	0.73	0.01	0.000106324	**
Compounds filtered	TRUE	FALSE	50	31	19	2	0.76	0.69	0.07	0.00011223	**
RPAIR class filtering	all	main	32	25	7	0	0.75	0.72	0.03	0.000279793	**
Graph type	RPAIR graph	ReactionGraph	8	8	0	0	0.74	0.57	0.17	0.004	*
Graph type	Reaction-specific RPAIR graph	ReactionGraph	8	8	0	0	0.72	0.57	0.15	0.004	*
RPAIR weight	RPAIR class-specific	Unit	40	20	20	8	0.74	0.73	0.01	0.016	
RPAIR class filtering	all	main-trans	28	18	10	4	0.75	0.74	0.01	0.088	
Directed	FALSE	TRUE	17	12	5	35	0.72	0.72	0	0.21	
											
Results for E. coli											
Compound weight	Degree	Unit	52	52	0	0	0.91	0.75	0.16	1.77E-10	**
Compounds filtered	TRUE	FALSE	50	27	23	2	0.87	0.8	0.07	0.000252206	**
RPAIR weight	RPAIR class-specific	Unit	33	24	9	15	0.86	0.84	0.02	0.000732117	**
Graph type	RPAIR graph	Reaction-specific RPAIR graph	36	27	9	12	0.85	0.84	0.01	0.003	*
Graph type	RPAIR graph	ReactionGraph	8	8	0	0	0.83	0.66	0.17	0.004	*
Graph type	Reaction-specific RPAIR graph	ReactionGraph	8	8	0	0	0.82	0.66	0.16	0.004	*
RPAIR class filtering	main	all	32	23	9	0	0.85	0.84	0.01	0.036	
RPAIR class filtering	main-trans	all	23	13	10	9	0.84	0.84	0	0.046	
RPAIR class filtering	main	main-trans	32	16	16	0	0.85	0.84	0.01	0.158	
Directed	FALSE	TRUE	11	6	5	41	0.83	0.83	0	0.482	

Results for S. cerevisiae											
Compound weight	Degree	Unit	52	48	4	0	0.61	0.48	0.13	3.18E-10	**
Compounds filtered	TRUE	FALSE	28	27	1	24	0.59	0.51	0.08	2.08E-06	**
RPAIR class filtering	all	main-trans	28	20	8	4	0.56	0.55	0.01	0.002	*
Graph type	RPAIR graph	ReactionGraph	8	8	0	0	0.57	0.45	0.12	0.007	
Graph type	Reaction-specific RPAIR graph	ReactionGraph	8	8	0	0	0.56	0.45	0.11	0.007	
RPAIR class filtering	main-trans	main	28	16	12	4	0.55	0.54	0.01	0.059	
RPAIR weight	RPAIR class-specific	Unit	26	17	9	22	0.56	0.55	0.01	0.131	
Directed	TRUE	FALSE	6	4	2	46	0.55	0.55	0	0.2	
Graph type	RPAIR graph	Reaction-specific RPAIR graph	27	15	12	21	0.55	0.55	0	0.605	
RPAIR class filtering	main	all	30	16	14	2	0.54	0.56	0.02	0.967	

Results for human											
Compound weight	Degree	Unit	52	46	6	0	0.63	0.55	0.08	1.14E-08	**
RPAIR class filtering	main-trans	main	32	30	2	0	0.63	0.55	0.08	7.80E-07	**
Compounds filtered	TRUE	FALSE	30	28	2	22	0.61	0.57	0.04	1.54E-06	**
RPAIR class filtering	all	main	32	30	2	0	0.64	0.55	0.09	2.37E-06	**
Graph type	RPAIR graph	Reaction-specific RPAIR graph	28	22	6	20	0.62	0.6	0.02	0.005	
Graph type	RPAIR graph	ReactionGraph	8	8	0	0	0.63	0.41	0.22	0.007	
Graph type	Reaction-specific RPAIR graph	ReactionGraph	8	8	0	0	0.61	0.41	0.2	0.007	
RPAIR weight	RPAIR class-specific	Unit	20	12	8	28	0.62	0.6	0.02	0.034	
RPAIR class filtering	all	main-trans	12	8	4	20	0.64	0.63	0.01	0.155	
Directed	FALSE	TRUE	10	6	4	42	0.6	0.59	0.01	0.305