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.

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.[4]

1. Data Processing 2. Statistical Analysis 3. Functional Enrichment Analysis
Peak detection Univariate analysis Over representation analysis
Retention time correction Dimension reduction Single sample profiling
Peak alignment Feature selection Quantitative enrichment analysis
Baseline filtering Cluster analysis
Data integrity check Classification 4. Metabolic Pathway Analysis
Missing value imputation Two-way ANOVA Enrichment analysis
ASCA Topology analysis
Temporal comparison Interactive 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),[5][6][7] DrugBank,[8][9][10] Toxin and Toxin-Target Database,[11] and The Small Molecule Pathway Database.[12] 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.

See also[edit]

References[edit]

  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. ^ "MetaboAnalyst: Overview". Archived from the original on 1 December 2011. Retrieved 17 January 2012.
  5. ^ 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.
  6. ^ 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
  7. ^ 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.
  8. ^ 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
  9. ^ 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.
  10. ^ 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.
  11. ^ 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
  12. ^ 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