Which Metabolic Pathways Generate and Characterize the Flux Space? A Comparison among Elementary Modes, Extreme Pathways and Minimal Generators

Table 1

Applications of network-based pathways analysis. Partially extracted from [4–6].

Applications	References
Identification of pathways	[7, 8]
Determination of minimal medium requirements	[9]
Analysis of pathway redundancy and robustness	[10–12]
Linkage between structure and regulation…
Correlated reactions (enzyme subsets)	[11, 13]
Detect excluding reaction pairs	[4]
Prediction of transcription ratios	[10, 14]
Include regulatory rules	[15]
Support for metabolic engineering…
Identification of pathways with optimal yields	[8]
Evaluation of effect of addition/deletion of genes	[16]
Inference of viability of mutants	[10, 17]
Detection of minimal cut sets	[18]
Suggest operations to increase product yield	[19]
Translation of a flux distribution into pathways activities…
Particular solution methods	[20, 21]
Alpha-spectrum	[22, 23]
Aid in the reconstruction of metabolic reaction networks…
Assignment of function to orphan genes	[24]
Detection of infeasible circles	[12, 25]
Detection of network dead ends	[9, 26, 27]
Support in the reconstruction of metabolic maps	[28]
Development of reduced, kinetic models	[29–31]