Hello,
One of my supervisors has run metabolomic analysis on mouse faecal samples for me. Metabolites have been quantified and I have run statistical tests to see which differ between genotypes.
At the moment, I have a list of significantly decreased and significantly increased metabolites. Is there a way to quickly see which pathways are most probably affected? I have been using MetaboAnalyst but am struggling.
Thanks
Dear Jamie
As far as I understood You need an enrichment analysis. MetaboAnalyst does this analysis very well, but if You have troubles using it, You can try this resource for the same purpose
http://impala.molgen.mpg.de
It's very intuitive, although I am not sure how much it is used compared to MetaboAnalyst, but You definitely can get at least some initial idea.
MetaboAnalyst is a good tool. There are many different analysis tools out thereto could try (see below)
Bu the faecal metabolite is not too well understood so interpret with caution. Peter Dorrenstein and Rob Knight have some nice work on linking the faecal metabolome with the faecal metagenome.
best wishes,
Elaine
Example softwares
Sugimoto M. Metabolomic pathway visualization tool outsourcing editing
function. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:7659-62. doi:
10.1109/EMBC.2015.7320166. PubMed PMID: 26738066.
or metabonetworks
Posma JM, et al. Bioinformatics. 2014 Mar 15;30(6):893-5. doi:
10.1093/bioinformatics/btt612. Epub 2013 Oct 30. PubMed PMID: 24177720;
or Shia & Wishart
MetPA https://doi.org/10.1093/bioinformatics/btq418
- Based on the list of significantly regulated metabolites, you can have the idea of pathway/s in which it is playing role. Apart from that, you can export your data files to MPP software for pathway analysis.
Metaboanalyst would provide an overview of significantly altrted pathways based on the total metabolite profile that you upload into the tool.
Data input does not need to be the significantly altered metabolites. It can the whole raw data.
Hope this works!
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