Question

How to update the list of genes mapped to GO terms in the topGO object?

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colaneri ▴ 30

@colaneri-7770

Last seen 5.6 years ago

United States

I understand that the annFUN function compiles the GO terms and map genes to those terms. However when I checked the number of genes annotated for a particular GO term in my topGO object, and I compared it with the AMIGO2 database, I noticed a big difference.

For example GO:0045665 have 82 genes in my topGO object but 227 in the AMIGO2 database.

Is there any way to get the most updated list of GO terms and genes in my topGO object?

I will appreciate the help

ALe

topgo go • 1.1k views

ADD COMMENT • link 7.7 years ago colaneri ▴ 30

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You will have to give more information than that. What species? If I go to amigo, there isn't any species with 227 genes for that term. Mouse is closest with 238. Human has 197, and if I look at the org.Hs.eg.db package, I get

> library(org.Hs.eg.db)
> con <- org.Hs.eg_dbconn()
> z <- dbGetQuery(con, "select * from go_all where go_id='GO:0045665';")
> dim(z)
[1] 198   4

> table(table(z[,1]))

  1   2
172  13

So for whatever reason there are duplicate gene IDs in there, but that's 185 genes for that term in the org.Hs.eg.db package that was built almost 6 months ago, versus 197 in amigo. I wouldn't be surprised if 12 more genes got annotated to a large-ish GO term in the intervening period, so that seems reasonable to me.

ADD REPLY • link 7.7 years ago James W. MacDonald 67k