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:

Tools that map and display metabolites and associated experimental data in visual representations of the metabolism (pathway mapping and visualization)
Tools that perform statistical analysis of metabolite annotations and/or associated quantitative data (metabolite enrichment analysis)

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