Metabolic pathway analysis

C. H. Schilling, S. Schuster, B. O. Palsson, and R. Heinrich, Metabolic pathway analysis Basic concepts and scientific applications in the post genomic era. Biotechnol. Prog. 15, 296 303 (1999). 

Metabolic pathway analysis A metabolic pathway is any sequence of feasible and observable biochemical reaction steps connecting a specified set of input and output metabolites. Unless a metabolite is observable independently, it is better lumped in with other metabolites and pathways. 

Clostridium thermocellum Anaerobe Metabolic labeling Metabolic pathway analysis (175)... 

Fusobacterium nucleatum Oral cavity microbe Label-free Metabolic pathway analysis (167)... 

Synechocystis sp. PCC6803 Phototroph iTRAQ Stress responses metabolic pathway analysis (212,213)... 

Methanococcus maripaludis Methanogen iTRAQ Metabolic pathway analysis (217)... 

Kromer JO, Wittmann C, Schroder H, Heinzle E (2006) Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab Eng 8(4) 353-369... 

Another resource that is useful in metabolic pathway analysis is the KEGG COMPOUND database of chemical compounds. This database is supplemented by the database of reaction information, which consists of REACTION, RPAIR, and ENZYME. The reaction formulas (chemical equations) in the ENZYME... 

Another two key concepts in metabolic engineering are metabolic pathway analysis and metabolic pathway modeling. The former is used for assessing inherent network properties in the complete biochemical reaction networks. It involves identification of the metabolic network structure (or pathway topology), quantification of the fluxes through the branches of the metabolic network, and identification of the control structures within the metabolic network. 

Metabolic pathway analysis. Users can also compare the ORFs in terms of metabolic pathways using ComPath (http //platcom.org/compath). 

Christophe H. Schilling, Stefan Schuster, Bernhard O. Palsson, Reinhart Heinrich, Metabolic Pathway Analysis Basic Concepts and Scientific Applications in the Post-genomic Era, Biotechnology Progress, 15 (1999), 296-303. 

Relationships among manipulated (controlled) variables, online measured variables, and product (uncontrolled) variables in most biosystems are nonlinear to some extent [95]. A forward model is when parameters, starting conditions, and relevant equations governing behavior are known, readily measurable inputs and the outputs are variables an inverse model is when the inputs are readily measurable variables and the outputs are difficult to measure parameters [69]. The forward model is most applicable to process validation, whereas the inverse model is most applicable to metabolic pathway analysis. Modeling systems such as neural networks have been used to describe the characteristics of extremely complex bioprocess systems [95]. 

Fairlamb AH. Metabolic pathway analysis in trypanosomes and malaria parasites. Philos Trans R Soc Lond B Biol Sci 2002 357(l417) 101-7. 

Rahman SA, Advani P, Schunk R et al. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 2005 21(7) 1189-1193. 

Toward Genome-Scale Metabolic Pathway Analysis 111... 

Trinh, C.T. and Thompson, R.A. (2012) Elementary mode analysis a useful metabolic pathway analysis tool for reprograming microbial metabolic pathways, in Reprogramming Microbial Metabolic Pathways, Vol. 64 (eds X. Wang, J. Chen, and P. Quinn), Springer Netherlands, Dordrecht, pp. 21 -42. 

Unrean, R, Nguyen, N.H., 2013. Metabolic pathway analysis and kinetic studies for production of nattokinase in Bacillus subtilis. Bioprocess Biosyst. Eng. 36, 45-56. 

Zhang, Q. and Xiu, Z. (2009) Metabolic pathway analysis of glycerol metabolism in Klebsiella pneumoniae incorporating oxygen regulatory system. Biotechnol. Progr, 25, 103-115. 

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