Center for Microbial Disease and Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
Curr Protoc Bioinformatics. 2020 Jun;70(1):e98. doi: 10.1002/cpbi.98.
MetaBridge is a web-based tool designed to facilitate the integration of metabolomics with other "omics" data types such as transcriptomics and proteomics. It uses data from the MetaCyc metabolic pathway database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to map metabolite compounds to directly interacting upstream or downstream enzymes in enzymatic reactions and metabolic pathways. The resulting list of enzymes can then be integrated with transcriptomics or proteomics data via protein-protein interaction networks to perform integrative multi-omics analyses. MetaBridge was developed to be intuitive and easy to use, requiring little to no prior computational experience. The protocols described here detail all steps involved in the use of MetaBridge, from preparing input data and performing metabolite mapping to utilizing the results to build a protein-protein interaction network. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Mapping metabolite data using MetaCyc identifiers Basic Protocol 2: Mapping metabolite data using KEGG identifiers Support Protocol 1: Converting compound names to HMDB IDs Support Protocol 2: Submitting mapped genes produced by MetaBridge for protein-protein interaction (PPI) network construction.
MetaBridge 是一个基于网络的工具，旨在促进代谢组学与其他“组学”数据类型（如转录组学和蛋白质组学）的整合。它使用来自 MetaCyc 代谢途径数据库和京都基因与基因组百科全书 (KEGG) 的数据，将代谢物化合物映射到酶促反应和代谢途径中直接相互作用的上游或下游酶。然后，可以通过蛋白质-蛋白质相互作用网络将生成的酶列表与转录组学或蛋白质组学数据集成，以执行综合多组学分析。MetaBridge 的开发旨在直观易用，几乎不需要事先的计算经验。这里描述的方案详细说明了使用 MetaBridge 的所有步骤，从准备输入数据和进行代谢物映射到利用结果构建蛋白质-蛋白质相互作用网络。© 2020 年由 John Wiley & Sons, Inc. 基本方案 1：使用 MetaCyc 标识符映射代谢物数据 基本方案 2：使用 KEGG 标识符映射代谢物数据 支持方案 1：将化合物名称转换为 HMDB IDs 支持方案 2：提交由 MetaBridge 生成的映射基因，用于蛋白质-蛋白质相互作用 (PPI) 网络构建。
