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	Unique best friends of superior value	Unique best friends of inferior value	Common best friends	Level of significance
Results for all organisms merged														
RPAIR class filtering	all	main	10	9	1	39	0.83	0.79	0.04	0.004	RPAIR graph; all	Reaction-specific RPAIR graph; main; Undirected	Reaction unit weight; Compound degree weight; Compounds unfiltered	*
Graph type	RPAIR graph	ReactionGraph	11	9	2	38	0.83	0.77	0.06	0.006	RPAIR graph; main-trans; Compounds unfiltered	ReactionGraph; all; Directed	Reaction unit weight; Compound degree weight	
Graph type	Reaction-specific RPAIR graph	ReactionGraph	9	8	1	40	0.82	0.77	0.05	0.006	Reaction-specific RPAIR graph; Compounds unfiltered	ReactionGraph; Directed	all; Reaction unit weight; Compound degree weight	
RPAIR class filtering	main-trans	main	8	7	1	41	0.83	0.79	0.04	0.01	RPAIR graph; main-trans	Reaction-specific RPAIR graph; main; Undirected	Reaction unit weight; Compound degree weight; Compounds unfiltered	
Graph type	RPAIR graph	Reaction-specific RPAIR graph	7	4	3	42	0.83	0.82	0.01	0.102	RPAIR graph; main-trans	Reaction-specific RPAIR graph; all	Reaction unit weight; Compound degree weight; Compounds unfiltered	
Compound weight	Degree	Unit	18	11	7	31	0.83	0.79	0.04	0.148	main-trans; Reaction unit weight; Compound degree weight; Compounds unfiltered	all; RPAIR class-specific weight; Compound unit weight; Compounds filtered	RPAIR graph	
RPAIR weight	RPAIR class-specific	Unit weight	3	2	1	46	0.82	0.83	0.01	0.605	all; RPAIR class-specific weight	main-trans; Reaction unit weight	RPAIR graph; Compound degree weight; Compounds unfiltered	
RPAIR class filtering	all	main-trans	4	2	2	45	0.83	0.83	0	0.821	all	main-trans	RPAIR graph; Reaction unit weight; Compound degree weight; Compounds unfiltered	
Directed	TRUE	FALSE	0	0	0	49	0.83	0.83	0	1	Directed	Undirected	RPAIR graph; main-trans; Reaction unit weight; Compound degree weight; Compounds unfiltered	
Compounds filtered	TRUE	FALSE	0	0	0	49	0.83	0.83	0	1	Compounds filtered	Compounds unfiltered	RPAIR graph; main-trans; Reaction unit weight; Compound degree weight	
														
Results for E. coli														
Graph type	RPAIR graph	ReactionGraph	4	4	0	24	0.95	0.89	0.06	0.05	RPAIR graph; Compounds unfiltered	ReactionGraph; all; Reaction unit weight; Directed	Compound degree weight	
RPAIR class filtering	main-trans	main	3	3	0	25	0.95	0.92	0.03	0.087	RPAIR graph; main-trans	main	Compound degree weight; Compounds unfiltered	
RPAIR class filtering	all	main	3	3	0	25	0.95	0.92	0.03	0.087	RPAIR graph; all; RPAIR class-specific weight	main	Compound degree weight; Compounds unfiltered	
Graph type	Reaction-specific RPAIR graph	ReactionGraph	3	3	0	25	0.94	0.89	0.05	0.091	Reaction-specific RPAIR graph; main-trans; RPAIR class-specific weight; Compounds unfiltered	ReactionGraph; all; Reaction unit weight; Directed	Compound degree weight	
Compound weight	Degree	Unit	6	4	2	22	0.95	0.91	0.04	0.417	Compound degree weight; Compounds unfiltered	all; RPAIR class-specific weight; Compound unit weight; Compounds filtered	RPAIR graph	
Graph type	RPAIR graph	Reaction-specific RPAIR graph	1	1	0	27	0.95	0.94	0.01	0.5	RPAIR graph	Reaction-specific RPAIR graph; main-trans; RPAIR class-specific weight	Compound degree weight; Compounds unfiltered	
RPAIR class filtering	all	main-trans	0	0	0	28	0.95	0.95	0	1	all; RPAIR class-specific weight	main-trans	RPAIR graph; Compound degree weight; Compounds unfiltered	
RPAIR weight	RPAIR class-specific	Unit weight	0	0	0	28	0.95	0.95	0	1	RPAIR class-specific weight	main-trans; Reaction unit weight	RPAIR graph; Compound degree weight; Compounds unfiltered	
Directed	TRUE	FALSE	0	0	0	28	0.95	0.95	0	1	Directed	Undirected	RPAIR graph; Compound degree weight; Compounds unfiltered	
Compounds filtered	TRUE	FALSE	0	0	0	28	0.95	0.95	0	1	Compounds filtered	Compounds unfiltered	RPAIR graph; Compound degree weight	
														
Results for S. cerevisiae														
RPAIR class filtering	all	main	6	5	1	5	0.66	0.6	0.06	0.147	all	RPAIR graph; main	Compound degree weight	
Compound weight	Degree	Unit	6	5	1	5	0.66	0.57	0.09	0.147	all; Compound degree weight	Compound unit weight; Compounds filtered		
Graph type	RPAIR graph	ReactionGraph	2	2	0	9	0.66	0.6	0.06	0.186	RPAIR graph	ReactionGraph; Directed	all; Reaction unit weight; Compound degree weight	
Graph type	Reaction-specific RPAIR graph	ReactionGraph	2	2	0	9	0.66	0.6	0.06	0.186	Reaction-specific RPAIR graph	ReactionGraph; Reaction unit weight; Directed	all; Compound degree weight	
RPAIR class filtering	all	main-trans	2	2	0	9	0.66	0.64	0.02	0.186	all	main-trans	Compound degree weight	
RPAIR class filtering	main-trans	main	4	3	1	7	0.64	0.6	0.04	0.29	main-trans	RPAIR graph; main	Compound degree weight	
Graph type	Reaction-specific RPAIR graph	RPAIR graph	0	0	0	11	0.66	0.66	0	1	Reaction-specific RPAIR graph	RPAIR graph; Reaction unit weight	all; Compound degree weight	
RPAIR weight	RPAIR class-specific	Unit weight	0	0	0	11	0.66	0.66	0	1	Reaction-specific RPAIR graph; RPAIR class-specific weight	Reaction unit weight	all; Compound degree weight	
Directed	TRUE	FALSE	0	0	0	11	0.66	0.66	0	1	Directed	Undirected	all; Compound degree weight	
Compounds filtered	TRUE	FALSE	0	0	0	11	0.66	0.66	0	1	Compounds filtered	Compounds unfiltered	all; Compound degree weight	
														
Results for human														
Graph type	RPAIR graph	ReactionGraph	5	4	1	5	0.7	0.63	0.07	0.089	RPAIR graph	ReactionGraph; all; Reaction unit weight; Directed	Compound degree weight	
Graph type	Reaction-specific RPAIR graph	ReactionGraph	4	3	1	6	0.7	0.63	0.07	0.101	Reaction-specific RPAIR graph	ReactionGraph; Reaction unit weight; Directed	all; Compound degree weight	
RPAIR class filtering	main-trans	main	2	1	1	8	0.7	0.65	0.05	0.5	RPAIR graph; main-trans	Reaction-specific RPAIR graph; main; Reaction unit weight; Undirected	Compound degree weight	
RPAIR class filtering	all	main	2	1	1	8	0.7	0.65	0.05	0.5	RPAIR graph; all	Reaction-specific RPAIR graph; main; Reaction unit weight; Undirected	Compound degree weight	
Compound weight	Degree	Unit	6	3	3	4	0.7	0.67	0.03	0.5	RPAIR graph; Compound degree weight	RPAIR class-specific weight; Compound unit weight; Compounds filtered		
Graph type	Reaction-specific RPAIR graph	RPAIR graph	2	1	1	8	0.7	0.7	0	0.814	Reaction-specific RPAIR graph; all	RPAIR graph	Compound degree weight	
RPAIR class filtering	all	main-trans	0	0	0	10	0.7	0.7	0	1	all	main-trans	RPAIR graph; Compound degree weight	
RPAIR weight	RPAIR class-specific	Unit weight	0	0	0	10	0.7	0.7	0	1	RPAIR class-specific weight	Reaction unit weight	RPAIR graph; Compound degree weight	
Directed	TRUE	FALSE	0	0	0	10	0.7	0.7	0	1	Directed	Undirected	RPAIR graph; Compound degree weight	
Compounds filtered	TRUE	FALSE	0	0	0	10	0.7	0.7	0	1	Compounds filtered	Compounds unfiltered	RPAIR graph; Compound degree weight