MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis.
Jasmine Chong,Othman Soufan,Carin Li,Iurie Caraus,Shuzhao Li,Guillaume Bourque,David S. Wishart,Jianguo Xia +7 more
TLDR
The user interface of MetaboAnalyst 4.0 has been reengineered to provide a more modern look and feel, as well as to give more space and flexibility to introduce new functions.Abstract:
We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major update in 2015, MetaboAnalyst has continued to evolve based on user feedback and technological advancements in the field. For this year's update, four new key features have been added to MetaboAnalyst 4.0, including: (1) real-time R command tracking and display coupled with the release of a companion MetaboAnalystR package; (2) a MS Peaks to Pathways module for prediction of pathway activity from untargeted mass spectral data using the mummichog algorithm; (3) a Biomarker Meta-analysis module for robust biomarker identification through the combination of multiple metabolomic datasets and (4) a Network Explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data. The user interface of MetaboAnalyst 4.0 has been reengineered to provide a more modern look and feel, as well as to give more space and flexibility to introduce new functions. The underlying knowledgebases (compound libraries, metabolite sets, and metabolic pathways) have also been updated based on the latest data from the Human Metabolome Database (HMDB). A Docker image of MetaboAnalyst is also available to facilitate download and local installation of MetaboAnalyst. MetaboAnalyst 4.0 is freely available at http://metaboanalyst.ca.read more
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MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights.
Zhiqiang Pang,Jasmine Chong,Guangyan Zhou,David Anderson de Lima Morais,Le Chang,Michel Barrette,Carol Gauthier,Pierre-Étienne Jacques,Shuzhao Li,Jianguo Xia +9 more
TL;DR: The MetaboAnalyst 5.0 as mentioned in this paper is the latest version of the web-based platform for comprehensive metabolomics data analysis and interpretation, aiming to narrow the gap from raw data to functional insights for global metabolomics based on HRMS.
Journal ArticleDOI
Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis.
TL;DR: An overview of the main functional modules and the general workflow of MetaboAnalyst 4.0 is provided, followed by 12 detailed protocols: © 2019 by John Wiley & Sons, Inc.
Journal ArticleDOI
Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.
TL;DR: This protocol details MicrobiomeAnalyst, a user-friendly, web-based platform for comprehensive statistical, functional, and meta-analysis of microbiome data, a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces.
Journal ArticleDOI
MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data.
Jasmine Chong,Jianguo Xia +1 more
TL;DR: A companion R package based on the R code base of the MetaboAnalyst web server to facilitate transparent, flexible and reproducible analysis of metabolomics data.
Journal ArticleDOI
Energy-stress-mediated AMPK activation inhibits ferroptosis.
Hyemin Lee,Fereshteh Zandkarimi,Yilei Zhang,Jitendra K. Meena,Jongchan Kim,Jongchan Kim,Li Zhuang,Siddhartha Tyagi,Li Ma,Thomas F. Westbrook,Gregory R. Steinberg,Daisuke Nakada,Brent R. Stockwell,Boyi Gan +13 more
TL;DR: It is found that ferroptotic cell death and lipid peroxidation can be inhibited by treatments that induce or mimic energy stress, and an unexpected coupling between ferroPTosis and AMPK-mediated energy-stress signalling is revealed.
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