Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation

Ari Rantanen; Hannu Maaheimo; Esa Pitkänen; Juho Rousu; Esko Ukkonen

doi:10.1007/11880646_9

Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation

Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen

University of Helsinki

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

1 Citation (Scopus)

Abstract

The most accurate estimates of the activity of metabolic pathways are obtained by conducting isotopomer tracer experiments. The success of this method, however, is intimately dependent on the quality and amount of data on isotopomer distributions of intermediate metabolites. In this paper we present a novel method for discovering sets of metabolite fragments that always have identical isotopomer distributions, regardless of the velocities of the reactions in the metabolic network. We outline several applications of this equivalence concept, including improved propagation of measurements, experiment planning and consistency checking of metabolic network. Our computational experiments in measurement propagation indicate that the improvement via the use of this technique may be substantial.

Original language	English
Title of host publication	Transactions on Computational Systems Biology VI
Editors	Corrado Priami, Gordon Plotkin
Place of Publication	Berlin - Heidelberg
Publisher	Springer
Pages	198-220
ISBN (Electronic)	978-3-540-46236-1
ISBN (Print)	978-3-540-45779-4
DOIs	https://doi.org/10.1007/11880646_9
Publication status	Published - 2006
MoE publication type	A4 Article in a conference publication

Publication series

Series	Transactions on Computational Systems Biology
Volume	VI
ISSN	1861-2075

Series	Lecture Notes in Computer Science
Volume	4420
ISSN	0302-9743

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10.1007/11880646_9

1 Citations
1 Conference article in proceedings

Flow analysis of metabolite fragments for flux estimation
Rantanen, A., Rousu, J., Pitkänen, E., Maaheimo, H. & Ukkonen, E., 2005, Proceedings of CMSB 2005.
Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

Cite this

Rantanen, Ari ; Maaheimo, Hannu ; Pitkänen, Esa et al. / Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation. Transactions on Computational Systems Biology VI. editor / Corrado Priami ; Gordon Plotkin. Berlin - Heidelberg : Springer, 2006. pp. 198-220 (Transactions on Computational Systems Biology, Vol. VI). (Lecture Notes in Computer Science, Vol. 4420).

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title = "Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation",

abstract = "The most accurate estimates of the activity of metabolic pathways are obtained by conducting isotopomer tracer experiments. The success of this method, however, is intimately dependent on the quality and amount of data on isotopomer distributions of intermediate metabolites. In this paper we present a novel method for discovering sets of metabolite fragments that always have identical isotopomer distributions, regardless of the velocities of the reactions in the metabolic network. We outline several applications of this equivalence concept, including improved propagation of measurements, experiment planning and consistency checking of metabolic network. Our computational experiments in measurement propagation indicate that the improvement via the use of this technique may be substantial.",

author = "Ari Rantanen and Hannu Maaheimo and Esa Pitk{\"a}nen and Juho Rousu and Esko Ukkonen",

note = "Preliminary version ”Flow analysis of metabolite fragments for flux estimation” appeared in the proceedings of CMSB 2005 (Third International Workshop on Computational Methods in Systems Biology), Edinburgh.",

year = "2006",

doi = "10.1007/11880646_9",

language = "English",

isbn = "978-3-540-45779-4",

series = "Transactions on Computational Systems Biology",

publisher = "Springer",

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Rantanen, A, Maaheimo, H, Pitkänen, E, Rousu, J & Ukkonen, E 2006, Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation. in C Priami & G Plotkin (eds), Transactions on Computational Systems Biology VI. Springer, Berlin - Heidelberg, Transactions on Computational Systems Biology, vol. VI, Lecture Notes in Computer Science, vol. 4420, pp. 198-220. https://doi.org/10.1007/11880646_9

Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation. / Rantanen, Ari; Maaheimo, Hannu; Pitkänen, Esa et al.
Transactions on Computational Systems Biology VI. ed. / Corrado Priami; Gordon Plotkin. Berlin - Heidelberg: Springer, 2006. p. 198-220 (Transactions on Computational Systems Biology, Vol. VI). (Lecture Notes in Computer Science, Vol. 4420).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

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T1 - Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation

AU - Rantanen, Ari

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AU - Rousu, Juho

AU - Ukkonen, Esko

N1 - Preliminary version ”Flow analysis of metabolite fragments for flux estimation” appeared in the proceedings of CMSB 2005 (Third International Workshop on Computational Methods in Systems Biology), Edinburgh.

PY - 2006

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N2 - The most accurate estimates of the activity of metabolic pathways are obtained by conducting isotopomer tracer experiments. The success of this method, however, is intimately dependent on the quality and amount of data on isotopomer distributions of intermediate metabolites. In this paper we present a novel method for discovering sets of metabolite fragments that always have identical isotopomer distributions, regardless of the velocities of the reactions in the metabolic network. We outline several applications of this equivalence concept, including improved propagation of measurements, experiment planning and consistency checking of metabolic network. Our computational experiments in measurement propagation indicate that the improvement via the use of this technique may be substantial.

AB - The most accurate estimates of the activity of metabolic pathways are obtained by conducting isotopomer tracer experiments. The success of this method, however, is intimately dependent on the quality and amount of data on isotopomer distributions of intermediate metabolites. In this paper we present a novel method for discovering sets of metabolite fragments that always have identical isotopomer distributions, regardless of the velocities of the reactions in the metabolic network. We outline several applications of this equivalence concept, including improved propagation of measurements, experiment planning and consistency checking of metabolic network. Our computational experiments in measurement propagation indicate that the improvement via the use of this technique may be substantial.

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DO - 10.1007/11880646_9

M3 - Conference article in proceedings

SN - 978-3-540-45779-4

T3 - Transactions on Computational Systems Biology

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Rantanen A, Maaheimo H, Pitkänen E, Rousu J, Ukkonen E. Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation. In Priami C, Plotkin G, editors, Transactions on Computational Systems Biology VI. Berlin - Heidelberg: Springer. 2006. p. 198-220. (Transactions on Computational Systems Biology, Vol. VI). (Lecture Notes in Computer Science, Vol. 4420). doi: 10.1007/11880646_9

Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation

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Flow analysis of metabolite fragments for flux estimation

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