MetaboAnalyst

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MetaboAnalyst [1] [2] [3] is a set of online tools for metabolomic data analysis and interpretation, created by members of the Wishart Research Group at the University of Alberta. It was first released in May 2009 and version 2.0 was released in January 2012. MetaboAnalyst provides a variety of analysis methods that have been tailored for metabolomic data. These methods include metabolomic data processing, normalization, multivariate statistical analysis, and data annotation. The current[ vague ] version is focused on biomarker discovery and classification.

The version 6.0 contains three new modules - tandem MS spectral processing and compound annotation, dose response analysis for chemical risk assessment, and leveraging metabolite-genome wide association analysis and Mendelian randomization for causal analysis. [4] [5]

MetaboAnalyst supports a wide variety of data input types commonly generated by metabolomic studies including GC/LC-MS raw spectra, MS/NMR peak lists, NMR/MS peak intensity table, NMR/MS spectral bins, and metabolite concentrations.

MetaboAnalyst has four modules:

  1. Data processing
  2. Statistical analysis (one-factor, two-factor, and time-series data)
  3. Functional enrichment analysis
  4. Metabolic pathway analysis

The table below summarizes the main features of each functional module. [6]

1. Data Processing2. Statistical Analysis3. Functional Enrichment Analysis
Peak detectionUnivariate analysisOver representation analysis
Retention time correctionDimension reductionSingle sample profiling
Peak alignmentFeature selectionQuantitative enrichment analysis
Baseline filteringCluster analysis
Data integrity checkClassification4. Metabolic Pathway Analysis
Missing value imputationTwo-way ANOVAEnrichment analysis
ASCATopology analysis
Temporal comparisonInteractive visualization

MetaboAnalyst generates a PDF report that includes a written record of each analysis step and displays results in graphical and tabular format. Users can also download processed data files and PNG image files.

MetaboAnalyst is part of a suite of metabolomics databases that also includes Human Metabolome Database (HMDB), [7] [8] [9] DrugBank, [10] [11] [12] Toxin and Toxin-Target Database, [13] and The Small Molecule Pathway Database. [14] The HMDB has over 7900 human metabolites and roughly 7200 associated DNA and protein sequences, that are linked to these metabolite entries. While DrugBank includes information on 6707 drugs and 4228 non-redundant drug targets, enzymes, transporters, and carriers, T3DB houses over 2900 common toxins and environmental pollutants. The suite is rounded out by SMPDB with its pathway diagrams for more than 350 human metabolic and disease pathways.

MetaboAnalyst has been used by >500,000 researchers worldwide since 2018. It currently receives >10,000 jobs submitted from >2000 users per weekday. [15]

See also

References

  1. ↑ Xia, J; Psychogios, N; Young, N; Wishart, DS (Jul 2009). "MetaboAnalyst: a web server for metabolomic data analysis and interpretation". Nucleic Acids Research. 37 (Web Server issue): W652-60. doi:10.1093/nar/gkp356. PMC   2703878 . PMID   19429898.
  2. ↑ Xia, J; Wishart, DS (Jun 2011). "Metabolomic data processing, analysis, and interpretation using MetaboAnalyst". Current Protocols in Bioinformatics. Chapter 14: Unit 14.10. doi:10.1002/0471250953.bi1410s34. PMID   21633943.
  3. ↑ Xia, J; Wishart, DS (Jun 2011). "Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst". Nature Protocols. 6 (6): 743–60. doi:10.1038/nprot.2011.319. PMID   21637195.
  4. ↑ "MetaboAnalyst6.0".
  5. ↑ Pang, Zhiqiang; Lu, Yao; Zhou, Guangyan; Hui, Fiona; Xu, Lei; Viau, Charles; Spigelman, Aliya F; MacDonald, Patrick E; Wishart, David S; Li, Shuzhao; Xia, Jianguo (2024-07-05). "MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation". Nucleic Acids Research. 52 (W1): W398 –W406. doi:10.1093/nar/gkae253. ISSN   0305-1048. PMC   11223798 . PMID   38587201.
  6. ↑ "MetaboAnalyst: Overview". Archived from the original on 1 December 2011. Retrieved 17 January 2012.
  7. ↑ Wishart, DS; Tzur, D; Knox, C; Eisner, R; Guo, AC; Young, N; Cheng, D; Jewell, K; Arndt, D; Sawhney, S; Fung, C; Nikolai, L; Lewis, M; Coutouly, MA; Forsythe, I; Tang, P; Shrivastava, S; Jeroncic, K; Stothard, P; Amegbey, G; Block, D; Hau, DD; Wagner, J; Miniaci, J; Clements, M; Gebremedhin, M; Guo, N; Zhang, Y; Duggan, GE; Macinnis, GD; Weljie, AM; Dowlatabadi, R; Bamforth, F; Clive, D; Greiner, R; Li, L; Marrie, T; Sykes, BD; Vogel, HJ; Querengesser, L (Jan 2007). "HMDB: the Human Metabolome Database". Nucleic Acids Research. 35 (Database issue): D521-6. doi:10.1093/nar/gkl923. PMC   1899095 . PMID   17202168.
  8. ↑ Wishart, DS; Knox, C; Guo, AC; Eisner, R; Young, N; Gautam, B; Hau, DD; Psychogios, N; Dong, E; Bouatra, S; Mandal, R; Sinelnikov, I; Xia, J; Jia, L; Cruz, JA; Lim, E; Sobsey, CA; Shrivastava, S; Huang, P; Liu, P; Fang, L; Peng, J; Fradette, R; Cheng, D; Tzur, D; Clements, M; Lewis, A; De Souza, A; Zuniga, A; Dawe, M; Xiong, Y; Clive, D; Greiner, R; Nazyrova, A; Shaykhutdinov, R; Li, L; Vogel, HJ; Forsythe, I (Jan 2009). "HMDB: a knowledgebase for the human metabolome". Nucleic Acids Research. 37 (Database issue): D603-10. doi:10.1093/nar/gkn810. PMC   2686599 . PMID   18953024. HMDB
  9. ↑ Forsythe, IJ; Wishart, DS (Mar 2009). "Exploring human metabolites using the human metabolome database". Current Protocols in Bioinformatics. Chapter 14: Unit14.8. doi:10.1002/0471250953.bi1408s25. PMID   19274632.
  10. ↑ Wishart, DS; Knox, C; Guo, AC; Shrivastava, S; Hassanali, M; Stothard, P; Chang, Z; Woolsey, J (2006-01-01). "DrugBank: a comprehensive resource for in silico drug discovery and exploration". Nucleic Acids Research. 34 (Database issue): D668-72. doi:10.1093/nar/gkj067. PMC   1347430 . PMID   16381955. DrugBank
  11. ↑ Wishart, DS; Knox, C; Guo, AC; Cheng, D; Shrivastava, S; Tzur, D; Gautam, B; Hassanali, M (Jan 2008). "DrugBank: a knowledgebase for drugs, drug actions and drug targets". Nucleic Acids Research. 36 (Database issue): D901-6. doi:10.1093/nar/gkm958. PMC   2238889 . PMID   18048412.
  12. ↑ Knox, C; Law, V; Jewison, T; Liu, P; Ly, S; Frolkis, A; Pon, A; Banco, K; Mak, C; Neveu, V; Djoumbou, Y; Eisner, R; Guo, AC; Wishart, DS (Jan 2011). "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs". Nucleic Acids Research. 39 (Database issue): D1035-41. doi:10.1093/nar/gkq1126. PMC   3013709 . PMID   21059682.
  13. ↑ Lim, E; Pon, A; Djoumbou, Y; Knox, C; Shrivastava, S; Guo, AC; Neveu, V; Wishart, DS (Jan 2010). "T3DB: a comprehensively annotated database of common toxins and their targets". Nucleic Acids Research. 38 (Database issue): D781-6. doi:10.1093/nar/gkp934. PMC   2808899 . PMID   19897546. T3DB
  14. ↑ Frolkis, A; Knox, C; Lim, E; Jewison, T; Law, V; Hau, DD; Liu, P; Gautam, B; Ly, S; Guo, AC; Xia, J; Liang, Y; Shrivastava, S; Wishart, DS (Jan 2010). "SMPDB: The Small Molecule Pathway Database". Nucleic Acids Research. 38 (Database issue): D480-7. doi:10.1093/nar/gkp1002. PMC   2808928 . PMID   19948758. SMPDB
  15. ↑ "User Statistics".
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