How to integrate GSEA (genes) and MSEA (metabolites) analysis ?

Question

[vin.darb]

Hello,

In order to find biomarkers of interest related to a disease (APS) and from two studies (one gene expression array study: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50395, and one NMR-metabolites study: https://www.ebi.ac.uk/metabolights/MTBLS356), my idea was to perform firstly a Gene Set Enrichissment Analysis (GSEA) from the first study and a Metabolites Set Enrichissment Anaalysis (MSEA) from the second study to put onlight some pathways of interest.

But after that, I was wondering of how integrate these 2 sets of datas in order to gain in sensitivity for the detection of biomarkers and pathways, in the case of a "multi-omics" approach.

I called for you're help because I'm a little lost. As a newly bioinformatics student I don't know all the softwares available and I do not even know if my idea is feasible.

Didi you know bioinformatics tools that can combine my two sets of data ? Maybe I shouldn't realise GSEA and MSEA and only considers the genes and metabolites differently expressed in the two studies before to combine them ?

Thank you by advance for you're help.

Answer 1

[Smandape]

One way I am doing it is by using pathways those represent metabolites and genes in them. This way I am using the same pathways as background for running enrichment analysis. Although, for doing this I had to write my own enrichment analysis script. I didn't find any tool that will do what I want.

The list of pathways was derived using a cytoscape plug in called metscape. Although, the list of pathways is only 70. One of my colleagues downloaded these pathways and helped me writing the statistical analysis script. Fisher's exact test was used for this analysis.

I am still trying to figure out if there is any other way to do this. I also found biocyc has multi-omics analysis pipeline take a look at it and see if its useful.

Good luck!