Hello everyone, I have used MS Peaks to Pathways feature at MetaboAnalyst online platform, to have an idea about which metabolites are in my samples, and which pathways are those metabolites are important in.
So, system gave me metabolite hits, and KEGG IDs of metabolites. And it also gave me plot of NES to -log10(p). (You can see it in the figure, each dot is a pathway) What does this plot means? Which pathways should I choose according to this plot?
Here are the basic explanations for MSEA/ GSEA: https://en.wikipedia.org/wiki/Metabolite_Set_Enrichment_Analysis and Article MSEA: A web-based tool to identify biologically meaningful p...
Thanks,
MSEA, like GSEA, is looking for significance by looking at multiple hits along a pathway - so for example if it sees several metabolites in the pyruvate pathway all unregulated (even by a little) it will score that as significant, even if the each individual metabolite was under the threshold for statistical significance. However, keep in mind a few things:
Peaks to pathways identifies the metabolites by looking for pathways, so it "stacks the deck" for known pathways. Because of that, it will have a hard time identifying metabolites that are not annotated to pathways, and often this can mean you are missing important information. Also, keep in mind that you can get a significant hit on a pathway with just a few metabolites, and this can cause misleading results if one of your metabolites is misidentified. In our experience, we found it better to use an approach such as STITCH that combined pathways and text-mining etc to connect metabolites into possible pathways.
Based on this plot, only pathways selected with a -log10(p) > 1.3 (p < 0.05) would be considered statistically significant. NES refers to normalized enrichment score calculated by GSEA/MSEA algorithms, which also indicates positive or negative associations.
In your plot, you should explore the pathways reflected by the three most significant at the right corner. MS Peaks to Pathways is based on the mummichog program, which is available at: http://mummichog-2.appspot.com/. You can also find more information on this program at http://mummichog.org/.
I hope this helps!
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