Investigation of kinetic-order sensitivities in metabolic reaction networks

Masatsugu Yamada, Masashi Iwanaga, Kansuporn Sriyudthsak, Masami Y. Hirai, Fumihide Shiraishi

研究成果: ジャーナルへの寄稿記事

抄録

Kinetic-order sensitivity (the ratio of relative change in a dependent variable to the relative change in a kinetic order in a power-law–type differential equation) has recently become an important indicator in metabolic pathway analysis using mathematical models with parameter values determined from time-series data on cellular metabolite concentrations. Here, we discuss a potential problem in calculating kinetic-order sensitivities. When the steady-state metabolite concentration is less than unity, a slight increase in the kinetic order changes the metabolite concentration in the incorrect direction, yielding a kinetic-order sensitivity value with an incorrect sign. This is caused by a property of the power-law function (y=Xn): when X is less than unity, y decreases for a larger positive n or for a smaller absolute value of negative n. We propose two solutions. The first is to directly calculate the kinetic-order sensitivities and then reverse the sign of the relevant value if a steady-state metabolite concentration less than unity is involved. The second involves calculation of the kinetic-order sensitivities after setting all metabolite concentrations to values greater than unity (e.g., by changing the units from mM to μM). The latter method changes the absolute values of the kinetic-order sensitivities according to the magnitude of a multiplication factor, because kinetic-order sensitivities do not have unique values. Nevertheless, since the normalized absolute values exhibit an almost identical distribution, it should not be difficult to identify which kinetic order has greater effect, although kinetic order rankings may change slightly under different calculation conditions.

元の言語英語
ページ(範囲)32-40
ページ数9
ジャーナルJournal of Theoretical Biology
415
DOI
出版物ステータス出版済み - 2 21 2017

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Reaction Network
Metabolic Network
Metabolic Networks and Pathways
Kinetics
kinetics
Metabolites
metabolites
Absolute value
Potential Problems
Time Series Data
biochemical pathways
Reverse
Time series
time series analysis
Pathway
Ranking
Multiplication
Power Law
Differential equations
Theoretical Models

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Modelling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

これを引用

Investigation of kinetic-order sensitivities in metabolic reaction networks. / Yamada, Masatsugu; Iwanaga, Masashi; Sriyudthsak, Kansuporn; Hirai, Masami Y.; Shiraishi, Fumihide.

:: Journal of Theoretical Biology, 巻 415, 21.02.2017, p. 32-40.

研究成果: ジャーナルへの寄稿記事

Yamada, Masatsugu ; Iwanaga, Masashi ; Sriyudthsak, Kansuporn ; Hirai, Masami Y. ; Shiraishi, Fumihide. / Investigation of kinetic-order sensitivities in metabolic reaction networks. :: Journal of Theoretical Biology. 2017 ; 巻 415. pp. 32-40.
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