MetaBridge: An Integrative Multi-Omics Tool for Metabolite-Enzyme Mapping

Q1 Biochemistry, Genetics and Molecular Biology

Current protocols in bioinformatics Pub Date : 2020-03-21 DOI:10.1002/cpbi.98

Travis Blimkie, Amy Huei-Yi Lee, Robert E.W. Hancock

{"title":"MetaBridge: An Integrative Multi-Omics Tool for Metabolite-Enzyme Mapping","authors":"Travis Blimkie, Amy Huei-Yi Lee, Robert E.W. Hancock","doi":"10.1002/cpbi.98","DOIUrl":null,"url":null,"abstract":"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 identifiersBasic Protocol 2: Mapping metabolite data using KEGG identifiersSupport Protocol 1: Converting compound names to HMDB IDsSupport Protocol 2: Submitting mapped genes produced by MetaBridge for protein-protein interaction (PPI) network construction","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"70 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2020-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.98","citationCount":"6","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current protocols in bioinformatics","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/cpbi.98","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}

引用次数: 6

Abstract

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

查看原文本刊更多论文

metbridge:代谢酶图谱的综合多组学工具

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)的数据来绘制代谢物化合物在酶反应和代谢途径中直接相互作用的上游或下游酶。由此产生的酶列表可以通过蛋白质-蛋白质相互作用网络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是为了直观和易于使用而开发的，几乎不需要事先的计算经验。本文描述的协议详细介绍了使用MetaBridge所涉及的所有步骤，从准备输入数据和执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 by John Wiley &基本协议1:使用MetaCyc标识符绘制代谢物数据基本协议2:使用KEGG标识符绘制代谢物数据支持协议1:将化合物名称转换为HMDB id支持协议2:提交MetaBridge生成的用于蛋白质-蛋白质相互作用(PPI)网络构建的映射基因

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Current protocols in bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

自引率

0.00%

发文量

期刊介绍： With Current Protocols in Bioinformatics, it"s easier than ever for the life scientist to become "fluent" in bioinformatics and master the exciting new frontiers opened up by DNA sequencing. Updated every three months in all formats, CPBI is constantly evolving to keep pace with the very latest discoveries and developments.