Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks
Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks
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DOI：
10.1093/nar/gkaa409
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发表时间：
2020-07-02
影响因子：
14.9
通讯作者：
Lobo, Daniel
中科院分区：
文献类型：
--
作者：
Hari, Archana;Lobo, Daniel
下一代测序已经为重建基因组规模的代谢网络铺平了道路，成为了解任何生物体中代谢回路的强大工具。然而，从这些由数千个反应和代谢物组成的大型网络中可视化和提取知识是目前需要用户友好工具的一个挑战。在这里，我们介绍了FLOXER(https://fluxer.umbc.edu)，)，这是一个免费和开放访问的新型Web应用程序，用于计算和可视化基因组规模的代谢流量网络。任何基于系统生物学标记语言的基因组规模的模型都可以上传到该工具，该工具自动执行通量平衡分析，并计算不同的通量图以进行可视化和分析。生物质生长或任何代谢物的生物合成的主要代谢途径可以被交互地剔除、分析并使用不同的布局以生成树、树状图或完整的图来可视化。此外，Floser可以计算并可视化任意两个代谢物或反应之间的k-最短代谢路径，以确定两个感兴趣的化合物之间的主要代谢路径。该网络应用程序包括从细菌到人类的各种生物的80个全基因组代谢重建，随时可供探索。Floser能够对基因组规模的代谢模型进行有效的分析和可视化，以发现关键的代谢途径。
Next-generation sequencing has paved the way for the reconstruction of genome-scale metabolic networks as a powerful tool for understanding metabolic circuits in any organism. However, the visualization and extraction of knowledge from these large networks comprising thousands of reactions and metabolites is a current challenge in need of user-friendly tools. Here we present Fluxer (https://fluxer.umbc.edu), a free and open-access novel web application for the computation and visualization of genome-scale metabolic flux networks. Any genome-scale model based on the Systems Biology Markup Language can be uploaded to the tool, which automatically performs Flux Balance Analysis and computes different flux graphs for visualization and analysis. The major metabolic pathways for biomass growth or for biosynthesis of any metabolite can be interactively knocked-out, analyzed and visualized as a spanning tree, dendrogram or complete graph using different layouts. In addition, Fluxer can compute and visualize the k-shortest metabolic paths between any two metabolites or reactions to identify the main metabolic routes between two compounds of interest. The web application includes >80 whole-genome metabolic reconstructions of diverse organisms from bacteria to human, readily available for exploration. Fluxer enables the efficient analysis and visualization of genome-scale metabolic models toward the discovery of key metabolic pathways.