Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01609, USA.
Genetics. 2021 Aug 26;219(1). doi: 10.1093/genetics/iyab089.
In our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology, and the response to therapeutic drugs. Visualization of the metabolic pathways that comprise the metabolic network is extremely useful for interpreting a wide variety of experiments. Detailed annotated metabolic pathway maps for C. elegans are mostly limited to pan-organismal maps, many with incomplete or inaccurate pathway and enzyme annotations. Here, we present WormPaths, which is composed of two parts: (1) the careful manual annotation of metabolic genes into pathways, categories, and levels, and (2) 62 pathway maps that include metabolites, metabolite structures, genes, reactions, and pathway connections between maps. These maps are available on the WormFlux website. We show that WormPaths provides easy-to-navigate maps and that the different levels in WormPaths can be used for metabolic pathway enrichment analysis of transcriptomic data. In the future, we envision further developing these maps to be more interactive, analogous to road maps that are available on mobile devices.
在我们的小组中，我们旨在了解秀丽隐杆线虫中的代谢及其与基因表达、生理学以及对治疗药物的反应之间的关系。可视化构成代谢网络的代谢途径对于解释各种实验非常有用。秀丽隐杆线虫的详细注释代谢途径图谱主要限于全生物体图谱，其中许多图谱的途径和酶注释不完整或不准确。在这里，我们提出了 WormPaths，它由两部分组成：（1）将代谢基因仔细手动注释到途径、类别和级别中，以及（2）62 条途径图谱，其中包括代谢物、代谢物结构、基因、反应和图谱之间的途径连接。这些图谱可在 WormFlux 网站上获得。我们表明，WormPaths 提供了易于导航的图谱，并且 WormPaths 中的不同级别可用于对转录组数据进行代谢途径富集分析。将来，我们设想进一步开发这些图谱，使其更具交互性，类似于移动设备上可用的路线图。
