how to metabolite enrichment analysis

[qqwxp]

The rWikiPathways vignettes tell us how to do a gene enrichment analysis by the gmt file, which give the gene lists per pathway.

Now I want to do the enrichment analysis based on the metabolome data. Is there a metabolites list file like gmt?

[DeniseSl22]

@qqwxp Thank you for your question; the GMT files are specifically for genes(and proteins). If you would like to perform a metabolomics analysis (in R), you could have a look at the scripts here: https://github.com/BiGCAT-UM/Transcriptomics_Metabolomics_Analysis/tree/master/metabolomics_analysis . These show how to perform preprocessing of the metabolomics data, identifiying the significantly changed metabolites, and perform pathway analysis (through our SPARQL endpoint). Hope this helps!