This is a test version of Biostars. For the public version, visit https://www.biostars.org.
gene enrichmnet analysis

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

r gene-enrichment-analysis
• 1,882 views • link
updated by Ram Ram • written by Eliza • Eliza

1 answer

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.

• 0 views • link
written by Apex92 • Apex92

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

enter image description here

• 0 views • link
written by Eliza • Eliza

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).

• 0 views • link
written by Apex92 • Apex92

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

enter image description here

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?

• 0 views • link
written by Eliza • Eliza

Log in to answer this question.

More posts like this