Hello!
My name is Sandra. I am a Master student and I am doing my MSc thesis with a PhD student. We are currently studying gene expression differences between endometriosis patients with and without recurrence. We have a ranked gene list from the microarray results and we want to analyse it and do a pathway enrichment to elucidate which pathways are most affected. We tried to do g:Profiler and then used EnrichmentMap with the not-ranked list of genes and the results were not good enough. Then we uploaded the ranked gene list to GSEA and used annotated gene sets downloaded from MSigDB and then EnrichmentMap. The results are not good, were better only using G:profiler and then EnrichmentMap.
We do not know how to do it and no one in our lab has done this before... Could you help us, please?
Thank you,
What do you mean by "results are not good?" Can you share what you got as result?
Sure! Here I show you the cytoscape results. These pathways are not really interesting in the case of endometriosis...
Wait, I can't uppload the image
I see, Indeed enrichment analysis is just a kind of statistical testing with no knowledge on why one is doing the test. Almost always one needs to inspect the enrichment result and pick those relevant pathways with their biological question for further analysis/discussion....
You used MSigDB for GSEA analysis but what gene sets did you use for gProfiler? if the gene sets are different then it is not surprising to get different results.