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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]