gravatar for drodavis0

4 hours ago by

Dear BioStars Community,

Wondered if anyone could offer some advice on GGProfiler2 and a question about background control for when I use it to do a gene set enrichment analysis (background referring to a gene list for comparison, I believe). Two of the options when using this package include to use "annotated" genes, which are "genes with at least one annotation." In contrast, the other option is "known", which is a list of all the known genes in the organism (see

When I compare my experimental gene list with "known" as background I get many more results with ggprofiler2 (which has functions for gene ontology, TRANSFAC analysis etc.), but when I use "annotated" I receive very little or no results. My inclination is to use "known", but I'm not sure if this is reliable or there are other considerations I should be having before just going with this.

Does anyone have any advice on or experience of this?

I really appreciate any advice or help people can offer - thanks!

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