A graph-theory-based method for processing of currency metabolites in metabolic networks
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    Abstract:

    Graph-theory-based pathway analysis is a commonly used method for pathway searching in genome-scale metabolic networks.However,such searching often results in many pathways biologically infeasible due to the presence of currency metabolites (e.g.H+,H2O,CO2,ATP etc.).Several methods have been proposed to address the problem but up to now there is no well-recognized methods for processing the currency metabolites.In this study,we proposed a new method based on the function of currency metabolites for transferring of functional groups such as phosphate.We processed most currency metabolites as pairs rather than individual metabolites,and ranked the pairs based on their importance in transferring functional groups,in order to make sure at least one main metabolite link exists for any reaction.The whole process can be done automatically by programming.Comparison with existing approaches indicates that more biologically infeasible pathways were removed by our method and the calculated pathways were more reliable,which may facilitate the graph-theory-based pathway design and visualization.

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高雅杰,袁倩倩,杨雪,毛志涛,余文童,刘浩,Igor Goryanin,马红武. 基于图论的代谢网络中流通代谢物处理新方法[J]. Chinese Journal of Biotechnology, 2022, 38(4): 1554-1564

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History
  • Received:June 01,2021
  • Revised:August 27,2021
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  • Online: April 22,2022
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