Table 2.

Effect of the penalty and metabolite constraints on relative flux range

Omics constraints	None		Transcriptomics		Metabolomics		Transcriptomics, metabolomics
Medium	Rich	Virulence	Rich	Virulence	Rich	Virulence	Rich	Virulence
Model genes with penalty	0	0	1258	1258	0	0	1258	1258
Model reactions with penalty	0	0	1996	1996	0	0	1996	1996
Reactions considereda	1587
Increased reactions (X > 1)	70		128		70		128
Decreased reactions (X < −1)	166		258		166		258
Remaining reactions (|X| < 1)	1351		1201		1351		1201
Metabolites consideredb	1397
Increased metabolites (X > 1)	28		74		28		74
Decreased metabolites (X < −1)	90		197		90		197
Remaining metabolites (|X| < 1)	1279		1126		1279		1126

^aModel reactions that were not implicated in loops that could carry flux greater than the solver tolerance in at least one condition were included.

^bAll model cellular metabolites that were not implicated in loops were included.