Question: Discrepancies between topGO output and input
0
gravatar for t.bergmann
5 months ago by
t.bergmann0
t.bergmann0 wrote:

Hey,

for my GO enrichment analyses I am using the topGO package. For my last analysis I discovered a discrepancy between the output from topGO for GO terms and the amount of actually annotated genes for these GO terms. For instance, topGO reports for the term 'defense response' 36 annotated genes of which 7 are significantly regulated, but if I search for these 36 genes I can only find 10 genes in my original input table where my gene IDs are connected to the GO-IDs. Has someone any idea on what this discrepancy might be based? I am thankful for any clue! Thank you in advance.

Kind regards.

go topgo enrichment gene ontology • 154 views
ADD COMMENTlink modified 5 months ago by James W. MacDonald52k • written 5 months ago by t.bergmann0
1

Could it be that some other genes are annotated to a GO term that implies this "defense response" term? I don't recall now if in this case the number of reported genes would be the ones directly annotated to a term or all that are linked to it.

ADD REPLYlink written 5 months ago by LluĂ­s Revilla Sancho530
Answer: Discrepancies between topGO output and input
2
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald52k wrote:

You have probably looked for the genes that are directly annotated to the GO term you mention, but that's not what topGO uses. GO is a directed acyclic graph, and all progeny terms are by default annotated to their ancestor, so you need to include all the progeny terms of defense response as well.

ADD COMMENTlink written 5 months ago by James W. MacDonald52k

Ok, thank you, this sounds plausible. I will check this!

ADD REPLYlink written 5 months ago by t.bergmann0
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