IPSJ Transactions on Bioinformatics
Online ISSN : 1882-6679
Single-atom Tracing in a Model Network of Carbohydrate Metabolism and Pathway Selection
Jun Ohta
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2018 Volume 11 Pages 1-13

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Abstract

Studies on computation of pathways connecting two metabolites have been reported. However, they did not intend to find pathways containing cycling, although there are biologically important cycles such as citric acid cycle (CAC). Whilst computation of pathways connecting two atoms, single-atom tracing, would contribute to finding pathways which include those containing cycling, it produces too many pathways to examine. The present article proposes a strategy to select pathways from those obtained by single-atom tracing, where coexistence of reactions on each pathway, specifically coexistence of a reaction and its reverse reaction forming a futile cycle together or reactions regulated in a reciprocal manner, is checked to select pathways based on biochemical meaning of the pathway. Using this strategy, 121 pathways were selected from total 7876 pathways from carbon atoms of glucose to CO2 in a model network of carbohydrate metabolism. The selected pathways included pathways using reactions or metabolites of CAC or pentose phosphate pathway multiple times. These results indicate that the proposed strategy can contribute to listing a limited number of pathways which include those containing cycling as possibly biochemically meaningful pathways.

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© 2018 by the Information Processing Society of Japan
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