Question: GO analysis and the universe set of genes
2
gravatar for tiago211287
4.2 years ago by
tiago2112871.1k
USA
tiago2112871.1k wrote:

I started to analyse GO enrichment with my genes list using the R package clusterProfiler, that get data from DAVID. Then, a doubt came out about what set of genes should I use in my universe when looking for enrichment?

All annotated genes?

Only annotated genes expressed in the tissue I am studying? (Mine is heart mouse)

Only genes present in my GTF file?

Thank you.

go R • 1.9k views
ADD COMMENTlink modified 4.2 years ago by Martombo2.6k • written 4.2 years ago by tiago2112871.1k

Enrichment analysis is based on comparing two lists and what these two lists should be depends on the question one asks. Which question are you interested in ?
1 - Does my list contain more genes of type X than expressed in the mouse heart ?
2- Does my list contain more genes of type X than found in my GTF file ?
Depending on the context (i.e. what the list and the GTF file represent), both are valid questions.
Typically, the background gene list is made of all genes tested in the experiment.

ADD REPLYlink written 4.2 years ago by Jean-Karim Heriche21k
0
gravatar for Martombo
4.2 years ago by
Martombo2.6k
Seville, ES
Martombo2.6k wrote:
filtering for genes that are expressed in your samples is a good idea. for example: if you have a neuroblastoma cell line and you pick randomly some genes that are expressed in it, you'll probably find some enrichment in neurological functions. using as background only genes that are expressed should correct for this bias.
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Martombo2.6k
of course the question of what threshold you use to say that a gene is expressed still remains.
ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Martombo2.6k
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