Computing Minimum Reaction Modifications in a Boolean Metabolic Network
Computing Minimum Reaction Modifications in a Boolean Metabolic Network
复制标题
计算布尔代谢网络中的最小反应修饰
DOI：
10.1109/tcbb.2017.2777456
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发表时间：
2017
期刊：
影响因子：
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通讯作者：
Tatsuya Akutsu
中科院分区：
文献类型：
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作者：
Takeyuki Tamura;Wei Lu;Jiangning Song;Tatsuya Akutsu
在代谢网络改造中，我们新加入酶或/和敲除基因，以最大限度地提高生物量的生产与最小的副作用。虽然这个问题已经研究了各种问题设置通过数学模型，包括通量平衡分析，基本模式，布尔模型，一些重要的问题设置仍然有待研究。在本文中，我们考虑布尔反应修改（BRM）问题，其中一个主机代谢网络和参考代谢网络中的布尔模型。宿主网络最初产生一些有毒化合物，不能产生一些必需的化合物，但参考网络可以产生必需的化合物，我们应该最小化从宿主网络中删除的反应和从参考网络中添加的反应的总数，以便在最终的宿主网络中不能产生有毒化合物，但可以产生必需的化合物。我们开发了基于整数线性规划（ILP）的BRM方法，并将其与OptStrain和SimOptStrain进行了比较。结果表明，我们的方法在减少添加和删除反应的总数方面表现更好，而OptStrain和SimOptStrain在优化目标化合物的生产方面表现更好。我们开发的软件可在“http://sunflower.kuicr.kyoto-u.ac.jp/~rogi/solBRM/solBRM.html“上免费获得。
In metabolic network modification, we newly add enzymes or/and knock-out genes to maximize the biomass production with minimum side-effect. Although this problem has been studied for various problem settings via mathematical models including flux balance analysis, elementary mode, and Boolean models, some important problem settings still remain to be studied. In this paper, we consider the Boolean Reaction Modification (BRM) problem, where a host metabolic network and a reference metabolic network are given in the Boolean model. The host network initially produces some toxic compounds and cannot produce some necessary compounds, but the reference network can produce the necessary compounds, and we should minimize the total number of removed reactions from the host network and added reactions from the reference network so that the toxic compounds are not producible, but the necessary compounds are producible in the resulting host network. We developed integer linear programming (ILP)-based methods for BRM, and compared them with OptStrain and SimOptStrain. The results show that our method performed better for reducing the total number of added and removed reactions, while OptStrain and SimOptStrain performed better for optimizing the production of the target compound. Our developed software is freely available at “http://sunflower.kuicr.kyoto-u.ac.jp/~rogi/solBRM/solBRM.html”.