How many genes is required for ORA analysis?

Question

[carolofharvest]

How many genes is required for ORA analysis?

I did pseudobulking on my single cell data and then I compared my conditions for specific cell type. I didn't get many significant results after doing deseq. I have only 10 genes significantly changed. Can ı use them in enrichment analysis ?

Answer 1

[Istvan Albert]

In general over-representation analysis is a brute force approach and once you have few genes the concepts don't apply.

For example a single gene even it is known to cause a phenotype will never come up via an ORA analysis.

As to how many you need - it all comes down to what kind of functions you have.

I would suggest using my tool, Genescape, I have designed it for this purpose to allow people to draw and visualize the functional content of smaller lists of genes

• GeneScape: A Python package for gene ontology visualization, JOSS, 2024