Journal ArticleDOI
Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst
TLDR
This protocol provides a step-wise description on how to format and upload data to MetaboAnalyst, how to process and normalize data,How to identify significant features and patterns through univariate and multivariate statistical methods and how to use metabolite set enrichment analysis and metabolic pathway analysis to help elucidate possible biological mechanisms.Abstract:
MetaboAnalyst is an integrated web-based platform for comprehensive analysis of quantitative metabolomic data. It is designed to be used by biologists (with little or no background in statistics) to perform a variety of complex metabolomic data analysis tasks. These include data processing, data normalization, statistical analysis and high-level functional interpretation. This protocol provides a step-wise description on how to format and upload data to MetaboAnalyst, how to process and normalize data, how to identify significant features and patterns through univariate and multivariate statistical methods and, finally, how to use metabolite set enrichment analysis and metabolic pathway analysis to help elucidate possible biological mechanisms. The complete protocol can be executed in approximately 45 min.read more
Citations
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Journal ArticleDOI
MetaboAnalyst 2.0—a comprehensive server for metabolomic data analysis
TL;DR: MetaboAnalyst 2.0 now contains dozens of new features and functions including new procedures for data filtering, data editing and data normalization and it also supports multi-group data analysis, two-factor analysis as well as time-series data analysis.
Journal ArticleDOI
A positive/negative ion–switching, targeted mass spectrometry–based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue
TL;DR: A quantitative polar metabolomics profiling platform using selected reaction monitoring with a 5500 QTRAP hybrid triple quadrupole mass spectrometer that covers all major metabolic pathways and is compatible with polar metabolites from any biological source.
Journal ArticleDOI
Metformin Retards Aging in C. elegans by Altering Microbial Folate and Methionine Metabolism
Filipe Cabreiro,Catherine Au,Kit-Yi Leung,Nuria Vergara-Irigaray,Helena M. Cochemé,Tahereh Noori,David Weinkove,Eugene Schuster,Nicholas D. E. Greene,David Gems +9 more
TL;DR: It is reported that metformin increases lifespan by altering microbial folate and methionine metabolism, consistent with action of this drug as a dietary restriction mimetic.
Journal ArticleDOI
Translational biomarker discovery in clinical metabolomics: an introductory tutorial
TL;DR: The concept of ROC curves are introduced and their use in single biomarker analysis for clinical chemistry is described and the meaning of area under R OC curves under AUC and partial AUC is explained, as well as the calculation of confidence intervals.
Journal ArticleDOI
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data
TL;DR: This protocol provides a step-wise description of how to effectively use NetworkAnalyst to perform network analysis and visualization from gene lists; to perform meta- analysis on gene expression data while taking into account multiple metadata parameters; and, finally, to perform a meta-analysis of multiple gene expressionData sets.
References
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