MetaboAnalyst 3.0—making metabolomics more meaningful

By Jianguo Xia, Igor Sinelnikov, Beomsoo Han, David S. Wishart. Nucleic Acids Res., 2015

2,584 citations recorded by the source corpus.

MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has experienced more than a 50X growth in user traffic (>50 000 jobs processed each month). In order to keep up with the rapidly increasing computational demands and a growing number of requests to support translational and systems biology applications, we performed a substantial rewrite and major feature upgrade of the server. The result is MetaboAnalyst 3.0. By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, we have been able substantially improve its performance, capacity and user interactivity. Three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites. In addition, popular features found in existing modules have been significantly enhanced by upgrading the graphical output, expanding the compound libraries and by adding support for more diverse organisms.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/a54a133562ca25a8955711f9292c2eedbeefb6c6

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Citations in the corpus

Metabolomics and isotope tracing (2018, methodology): “Such plots can be generated by free software like MetaboAnalyst (Xia et al., 2015).”
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights (2021, background): “0 focused on translational biomarker analysis (13) and addressed the performance bottleneck by leveraging cloud computing and modern web technologies (14).”
NOREVA: normalization and evaluation of MS-based metabolomics data (2017, methodology): “NOREVA stood out among available tools by providing sequential strategy integrating the QCS-based signal correction with normalization methods (19,47) and removing unwanted variations based on IS and QCM (18,28).”
Metabolite profiling of symbiont and host during thermal stress and bleaching in the coral Acropora aspera (2017, methodology): “Metabolite data extraction and analysis were undertaken based on the protocol described in Dias et al. (2015) with the software package MetaboAnalyst 3.0 (Xia et al. 2015).”
Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity (2016, methodology): “The second method used to perform pathway-enrichment analysis is ‘‘MetaboAnalyst’’ (Xia et al., 2015), which does allow the definition of such a background set.”
Computational approaches in target identification and drug discovery (2016, methodology): “Tools such as thehuman metabolomedatabase [22] and MetaboAnalyst [23] support integrative omics pathway analysis.”
Metabolomics and fish nutrition: a review in the context of sustainable feed development (2018, background): “Information about metabolic pathway analyses have been even integrated into metabolomic software analysis to directly help interpretation of a given metabolite (Xia et al. 2015).”
Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis (2016, methodology): “The latest version of the server, MetaboAnalyst 3.0 (Xia et al., 2015), incorporated a new Web framework and cloud server for improved performance.”
Pathview Web: user friendly pathway visualization and data integration (2017, methodology): “While the combined analysis has been implemented previously (24,25), Pathview Web server makes such analysis possible for a wide range of species and data types.”