How to map metabolomics data in the context of metabolic pathways ?
Since metabolites belonging to a fingerprint may appear in several metabolic pathways, we will also introduce and use pathaway enrichment to identify most significant pathways.
At the end of the course, you wil be able to :
- list pathways where at least on metabolite of the fingerprint is found
- interpret pathway enrichment results and thus identify siginficant pathways
- know the limit of metabolic pathways
Knowing the notion of metabolic pathway.
Metabolic pathways divide metabolism into functional modules. They provide a good background to provide a functional interpretation of a metabolic fingerprints. In this section we will define the notion of pathways, see how we can measure if they are significatively enriched for a given fingerprint. We will also discuss the limits of pathways.
In this section we will define the notion of pathways, see how we can
measure if they are significatively enriched for a given fingerprint. We
will also discuss the limits of pathways.
Metabolic pathways provide a functional overview of a metabolic fingerprint. Pathway enrichment, even if it presents limitations in the context of metabolomics, allows identifying pathways of interest. Nevertheless, pathways are subjective modules and metabolic modulations may span several pathways. This is the reason why it is of interest to analyse fingerprints in a more holistic manner using metabolic network formalism.
- Kanehisa,M., Furumichi,M., Tanabe,M., Sato,Y., Morishima,K. (2017). KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res., 45, D353–D361. https://dx.doi.org/10.1093%2Fnar%2Fgkw1092
- Kankainen,M., Gopalacharyulu,P., Holm,L. Oresic,M. (2011). MPEA--metabolite pathway enrichment analysis. Bioinformatics, 27, 1878–9. https://doi.org/10.1093/bioinformatics/btr278