Gene enrichment analysis

Question

[Eliza]

Hi , I'm trying to do a go enrichment analysis in R using the GofuncR packagehttps://rpubs.com/Akhil_Velluva/GOfuncR . I have list of genes that I want to test, but I want to preform this test using my own list of genes as the "universe". I'm a little bit confused where do I specify my "universe " genes ? Are they the "background" in the link of the package ?

Thanks

[Meisam]

If you want to find enrichment of your selected genes versus the superset of all genes detected, then yes you mean the background. And to do that as indicated in the package manual you need to modify the dataframe you feed as "genes" to the go_enrich() function.

[ATpoint]

I cannot speak for this package but I recommend clusterProfiler where the universe argument isindeed all tested genes so your background.

Answer 1

[nux]

Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and non-candidate (background).

example:

gene1 0
gene2 1
gene3 0
gene4 0

....

So Geneset should be defined as Gs = {g1 .. gn} and genes to test are elements of Gs with value 1

This will test the overrepresentation of gene 2 across that set.

[Eliza]

nux Hi thank you for yor answer , basically what i have is a data frame of 8000 genes from them 200 are with p value <0.05 ant a list of refrence genes for a certain disease . what i noticed in GofuncR and in here :http://geneontology.org/ that i can only specify the input genes as the analyed list and my own reference list for a certain disease as background but i cant also add as an input my own list of 8000 genes as the N variable in the hyper geometric distibution that the test is based on . Is there any way to do this in GofuncR or the website or any othe packge ?