annotation for a gene set enrichment analysis

Question

[h.botond]

Hello everybody

I want to do a gene set enrichment analysis. Therefore, in the firest step, I assigned my proteins into COG, NOG categories. But some proteins has multiple COG, NOG categories. Which I thing is normal.

The problem is that I don't know how to handle these proteins in the next step. I think when I will perform the gene set enrichment analysis they will form small groups which in the end will bias the result.

What should I do to avoid this?

Thank for every suggestion.

Answer 1

[Istvan Albert]

Multifunctionality of proteins is very common and is a confounding factor as you suspect. Here is how ErmineJ deals with it

[h.botond]

Thank for the quick and useful response. I will check the program. Did you use before? Is it useful for bacterial RNA-Seq transcriptome analysis?