Arabzadeh Mona, Saheb Zamani Morteza, Sedighi Mehdi, Marashi Sayed-Amir
Department of Computer Engineering and Information Technology, Amirkabir University of Technology, Tehran, Iran.
Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.
Biosystems. 2018 Mar;165:40-51. doi: 10.1016/j.biosystems.2017.12.001. Epub 2018 Jan 12.
An elementary flux mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to find a subset of EFMs is proposed based on a graph data model. The given metabolic network is mapped to the graph model and decisions for reaction inclusion can be made based on metabolites and their associated reactions. This notion makes the approach more convenient to categorize the output pathways. Implications of the proposed method on metabolic networks are discussed.
基本通量模式（EFM）是在稳态约束空间中起作用的具有最小反应集的途径。由于计算EFM的计算复杂度很高，因此已经提出了不同的方法来找到这些通量平衡途径。本文提出了一种基于图数据模型来找到EFM子集的方法。将给定的代谢网络映射到图模型上，并且可以基于代谢物及其相关反应来做出反应纳入的决策。这一概念使得该方法更便于对输出途径进行分类。文中讨论了所提出方法对代谢网络的影响。
