An interval approach for dealing with flux distributions and elementary modes activity patterns. (English) Zbl 1451.92150

Llaneras, F.; Picó, J.

J. Theor. Biol. 246, No. 2, 290-308 (2007).

Summary: This work introduces the use of an interval representation of fluxes. This representation can be useful in two common situations: (a) when fluxes are uncertain due to the lack of accurate measurements and (b) when the flux distribution is partially unknown. In addition, the interval representation can be used for other purposes such as dealing with inconsistency or representing a range of behaviour.
Two main problems are addressed. On the one hand, the translation of a metabolic flux distribution into an elementary modes or extreme pathways activity pattern is analysed. In general, there is not a unique solution for this problem but a range of solutions. To represent the whole solution region in an easy way, it is possible to compute the \(\alpha\)-spectrum (i.e., the range of possible values for each elementary mode or extreme pathway activity). Herein, a method is proposed which, based on the interval representation of fluxes, makes it possible to compute the \(\alpha\)-spectrum from an uncertain or even partially unknown flux distribution.
On the other hand, the concept of the flux-spectrum is introduced as a variant of the metabolic flux analysis methodology that presents some advantages: applicable when measurements are insufficient (underdetermined case), integration of uncertain measurements, inclusion of irreversibility constraints and an alternative procedure to deal with inconsistency. Frequently, when applying metabolic flux analysis the available measurements are insufficient and/or uncertain and the complete flux distribution cannot be uniquely calculated. The method proposed here allows the determination of the ranges of possible values for each non-calculable flux, resulting in a flux region called flux-spectrum.
In order to illustrate the proposed methods, the example of the metabolic network of CHO cells cultivated in stirred flasks is used.

MSC:

92C42	Systems biology, networks
92C37	Cell biology

Keywords:

\(\alpha\)-spectrum; elementary modes; extreme pathways; metabolic flux analysis

Software:

Metatool; YANA

References:

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