gene enrichmnet analysis

Question

[Eliza]

Hi,

I have a list of genes from my experiment and i want to perform gene enrichment analysis. I also have a list of background genes associated with a specific disease. I was wondering if there is a tool in which I can preform the analysis in a way that the disease from the background list becomes sort of "Go enrichment term"?

Thank you

Answer 1

[Apex92]

You can try to do it using gpofiler2. Here is the link (https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html).

Another option can be Clusterprofiler as well.

[Eliza]

so just to make sure this tools can use the diasese name assosiated with my background list as a node name ?

[Apex92]

Yes, you can set a custom background set in the gprofiler2 (I have not checked the other tool recently but I remember that it was possible to do).

[Eliza]

I tried as you sujjested , this is what i got :

the gens in my background list are associated with a disease called:ectodermal dysplasia what i whished that the name of the disease would be a row in the column "term_name" , is it possible with gptofiler2?