I have a curated gene list using which I would like to carry out enrichment analysis on DE genes in clusters obtained using Seurat. I first tried to do this manually using Fisher Exact test like so:
No. genes in curated list: 5840 No. DE genes in Cluster 0 (from Seurat): 512 No. Overlap genes: 209 No. Universe: 23,000 No. Untested: 23000 - (5631+209+303) = 16857
5840-209=5631 512-209=303
2X2 contingency table is designed as such:
209 5631 303 16857
The odds ratio looks off in this case so I am wondering if I designed the test correctly?
Secondly, I was trying to find a package (like fsgea) in R that would let me do this kind of analysis. My idea was to use all DE genes in each cluster to be fed as a custom pathway. But I am confused about the ranked list? What should that be? Unable to figure out where the curated gene list fit into the equation. Alternatively, is there a better approach to address this issue?
I can highly recommend https://amp.pharm.mssm.edu/Enrichr/ . It's very easy to use, and has a great amount of gene-set libraries. There is also an R package that works very well called EnrichR https://cran.r-project.org/web/packages/enrichR/index.html .
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