物质图是新陈代谢的最佳简单图表示
Substance graphs are optimal simple-graph representations of metabolism
摘要：
研究生物化学系统组织的一种方法是使用统计图论。即使在这样一个高度简化的方法中，它忽略了生物化学的大部分动态方面，人们也面临着基本的问题，例如如何将化学反应系统简化为一个图，保留尽可能多的原始反应系统的功能信息。在这样的图形表示中，边应该在衬底和产品之间，或者衬底和衬底之间，或者两者之间？顶点应该代表物质还是反应？不同的定义编码了关于反应系统的不同信息。在本文中，我们评估四种不同的图形表示的新陈代谢，适用于不同的生物体和数据库的数据。通过比较聚类（网络模块）和注释功能之间的重叠，以及通过将已识别的货币代谢物与其他作者使用定性生物学参数识别的代谢物进行比较，来评估图形表示。我们发现，一个“物质网络”，其中所有参与反应的代谢物是连接的，是相对较好的比别人，评估模块和功能之间的功能重叠和识别货币代谢物的数量和身份。
英文摘要：
One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental questions, such as how the chemical reaction systems should be reduced to a graph retaining as much functional information as possible from the original reaction system. In such graph representations, should the edges go between substrates and products, or substrates and substrates, or both? Should vertices represent substances or reactions? Different definitions encode different information about the reaction system. In this paper we evaluate four different graph representations of metabolism, applied to data from different organisms and databases. The graph representations are evaluated by comparing the overlap between clusters (network modules) and annotated functions, and also by comparing the set of identified currency metabolites with those that other authors have identified using qualitative biological arguments. We find that a "substance network," where all metabolites participating in a reaction are connected, is relatively better than others, evaluated both with respect to the functional overlap between modules and functions and to the number and identity of identified currency metabolites.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
