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Tools for the functional interpretation of metabolomic experiments

Omics approaches (e.g genomics, transcriptomics, proteomics) seek to massively characterizing the molecular repertories of living systems. Among them, metabolomics tries to determine the set of metabolites in a given biological system. As metabolomic techniques develop and allow characterizing larger sets of metabolites, researchers need automatic methods to interpret their experimental results.

We can classify these tools in two groups:

More information and links

  • Monica Chagoyen and Florencio Pazos (2013). Tools for the functional interpretation of metabolomic experiments. Briefings in Bioinformatics. 14(6):737-744.
    [PubMed:23063930] [HTML] [PDF]
  • Mónica Chagoyen, Javier López-Ibáñez, Florencio Pazos (2016). Functional Analysis of Metabolomics Data. Methods Mol Biol. 1415:399-406.
    [PubMed:27115644] [HTML] [PDF]
  • Metabolomics (Wikipedia)
  • Servers and tools

    Pathway mapping and visualization
    Name URL
    BioCyc - Omics Viewer http://biocyc.org
    iPath http://pathways.embl.de
    KaPPA-View http://kpv.kazusa.or.jp/en/
    KEGG http://www.genome.jp/kegg/pathway.html
    MapMan http://mapman.gabipd.org/web/guest/mapman
    MetPA http://metpa.metabolomics.ca
    Metscape http://metscape.ncibi.org
    MGV http://www.microarray-analysis.org/mayday
    Paintomics http://www.paintomics.org
    Pathos http://motif.gla.ac.uk/Pathos/
    Pathvisio http://www.pathvisio.org/
    ProMetra http://www.cebitec.uni-bielefeld.de/groups/brf/software/prometra_info/
    Reactome http://www.reactome.org
    VANTED http://vanted.ipk-gatersleben.de

    Metabolite enrichment analysis
    Name URL
    IMPaLA http://impala.molgen.mpg.de
    MBROLE 2.0 http://csbg.cnb.csic.es/mbrole2
    MPEA http://ekhidna.biocenter.helsinki.fi/poxo/mpea/
    MSEA http://www.msea.ca

    © 2012, Computational Systems Biology Group. CNB-CSIC