Background for enrichr about gget

[lauraluebbert]

Hi GJ,

I am not sure I understand your request. Could you please describe how you would do this on the Enrichr website?

Best,

Laura

[gjhuizing]

Hi! Thanks for the quick answer.

By background I mean the universe or statistical domain of reference. I'm no expert in GSEA but from what I understood it should in some cases be smaller than the whole genome (e.g. only the genes whose expression is detected in the experiment). See [1] at "remaining questions, section 4".

After searching a bit, it seems that Enrichr actually doesn't have that option. So feel free to mark this as solved :)

Maybe that is why Scanpy chose to have g:Profiler in their API https://biit.cs.ut.ee/gprofiler/gost ? There is an explanation on the statistical domain in section "Statistical domain scope" of https://biit.cs.ut.ee/gprofiler/page/docs.

Best
GJ

[1] Huang, Da Wei, Brad T. Sherman, and Richard A. Lempicki. "Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists." Nucleic acids research 37.1 (2009): 1-13.

[anhchi172]

Hi GJ,

Thank you for your suggestion. The new release v0.27.9 of gget now a new background_list argument for users to provide a list of background genes for gget enrichr. You can install the latest version of gget using the command

pip install gget

Let us know if there are any issues.

Best regards,
Chi