Using Pathway Covering to Explore Connections among Metabolites
Using Pathway Covering to Explore Connections among Metabolites
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DOI：
10.3390/metabo9050088
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发表时间：
2019-05-01
期刊：
影响因子：
4.1
通讯作者：
Karp, Peter D.
中科院分区：
文献类型：
--
作者：
Midford, Peter E.;Latendresse, Mario;Karp, Peter D.
解释代谢物丰度响应于实验治疗或疾病状态的变化仍然是代谢组学的主要挑战。路径覆盖是一种新的算法，它采用代谢物（化合物）列表，并确定生物体中包括（覆盖）列表中所有代谢物的最小成本代谢途径集。我们使用了五个函数来分配路径的成本，包括为所有路径分配一个常数，这会产生一个具有最小路径计数的解决方案;两种方法惩罚大的路径;一种方法基于路径的分配功能偏好路径，另一种方法松散地对应于代谢通量。通过算法计算的途径覆盖集可以显示为多途径图（途径拼贴），突出显示覆盖的代谢物。我们使用来自Metabolomics的几个数据集研究了路径覆盖算法。该算法最适用于具有显著统计学和倍数变化的代谢物列表，每种代谢物具有指定的变化方向。途径覆盖算法现在可在Pathway Tools软件和BioCyc网站中获得。
Interpreting changes in metabolite abundance in response to experimental treatments or disease states remains a major challenge in metabolomics. Pathway Covering is a new algorithm that takes a list of metabolites (compounds) and determines a minimum-cost set of metabolic pathways in an organism that includes (covers) all the metabolites in the list. We used five functions for assigning costs to pathways, including assigning a constant for all pathways, which yields a solution with the smallest pathway count; two methods that penalize large pathways; one that prefers pathways based on the pathway's assigned function, and one that loosely corresponds to metabolic flux. The pathway covering set computed by the algorithm can be displayed as a multi-pathway diagram (pathway collage) that highlights the covered metabolites. We investigated the pathway covering algorithm by using several datasets from the Metabolomics Workbench. The algorithm is best applied to a list of metabolites with significant statistics and fold-changes with a specified direction of change for each metabolite. The pathway covering algorithm is now available within the Pathway Tools software and BioCyc website.