MetaboAnalyst 2.0—a comprehensive server for metabolomic data analysis

By Jianguo Xia, R. Mandal, Igor Sinelnikov, David Broadhurst, David S. Wishart. Nucleic Acids Res., 2012

1,162 citations recorded by the source corpus.

First released in 2009, MetaboAnalyst (www.metaboanalyst.ca) was a relatively simple web server designed to facilitate metabolomic data processing and statistical analysis. With continuing advances in metabolomics along with constant user feedback, it became clear that a substantial upgrade to the original server was necessary. MetaboAnalyst 2.0, which is the successor to MetaboAnalyst, represents just such an upgrade. MetaboAnalyst 2.0 now contains dozens of new features and functions including new procedures for data filtering, data editing and data normalization. It also supports multi-group data analysis, two-factor analysis as well as time-series data analysis. These new functions have also been supplemented with: (i) a quality-control module that allows users to evaluate their data quality before conducting any analysis, (ii) a functional enrichment analysis module that allows users to identify biologically meaningful patterns using metabolite set enrichment analysis and (iii) a metabolic pathway analysis module that allows users to perform pathway analysis and visualization for 15 different model organisms. In developing MetaboAnalyst 2.0 we have also substantially improved its graphical presentation tools. All images are now generated using anti-aliasing and are available over a range of resolutions, sizes and formats (PNG, TIFF, PDF, PostScript, or SVG). To improve its performance, MetaboAnalyst 2.0 is now hosted on a much more powerful server with substantially modified code to take advantage the server’s multi-core CPUs for computationally intensive tasks. MetaboAnalyst 2.0 also maintains a collection of 50 or more FAQs and more than a dozen tutorials compiled from user queries and requests. A downloadable version of MetaboAnalyst 2.0, along detailed instructions for local installation is now available as well.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/ad20e8df2cb032c0f2164892e251856c4edc2def

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Citations in the corpus

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights (2021, neutral): “analysis for targeted metabolomics (12).”
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database (2013, background): “We have also corrected and added much more physiological (tissue, organ, organelle and transporter) information, substantially improved its visual interactivity and quality, created downloadable BioPAX pathway ﬁles for all of SMPDB’s pathways and increased SMPDB’s visibility by integrating SMPDB int”
NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration (2014, background): “…been significant progress in the development of web-based tools that support processing and statistical analysis for data from various omics experiments (38,39), user-friendly and web-based tools to assist bench researchers and clinicians in performing complex network analysis are still lacking.”
Metabolomics Analysis Reveals the Salt-Tolerant Mechanism in Glycine soja (2017, methodology): “The rest of the replicates were used to determine a number of growth indices under each treatment.”
MetaboAnalyst 3.0—making metabolomics more meaningful (2015, background): “The second version of MetaboAnalyst (released in 2012) contained four functional modules that supported expanded capabilities in metabolomic functional analysis and data interpretation (2).”
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis (2018, methodology): “0, which was released in 2012 (2), incorporated three new modules for metabolite set enrichment analysis (MSEA) (3), metabolic pathway analysis (MetPA) (4), as well as advanced twofactor and time-series analyses (MetATT) (5).”
Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis (2016, methodology): “The second version of the Web server, MetaboAnalyst 2.0 (Xia et al., 2012), incorporated additional components for functional analyses such as metabolic pathway analysis, or MetPA (Xia and Wishart, 2010a) and metabolite set enrichment analysis, or MSEA (Xia and Wishart, 2010b).”
Multivariate Analysis in Metabolomics. (2012, background): “Xia J, Mandal R, Sinelnikov IV, Broadhurst D, Wishart DS. MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis.”
Analytical Methods in Untargeted Metabolomics: State of the Art in 2015 (2015, neutral): “Web MS and NMR 1–7 http://www.metaboanalyst.ca/ Xia et al. (2012) XCMS R MS 1–3 http://metlin.scripps.edu/xcms/ Smith et al. (2006) MAIT R LC-MS 1–5 http://b2slab.upc.edu/software-and-downloads Fernández-Albert et al. (2014) OpenMS Application LC-MS 1–3 http://open-ms.sourceforge.net/ Sturm et al.…”
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data (2015, methodology): “Comparison with other available tools for data integration Many excellent web-based tools exist for analyzing a single omics data set, such as GEPAS 18 , GenePattern 19 , MetaboAnalyst 20,21 and so on.”