How to retreive all the genes belonging to one GO term

Question

[Francois Piumi]

Hi,

I'd like to retreive all the genes belonging to a GO term.

I tried : (R language)

library(org.Hs.eg.db)

xx <- as.list(org.Hs.egGO2ALLEGS)

xx is a list of GO terms, and for each GO term there's a list of the corresponding genes with an "entrezID" format.

The problem is that when I check this output on other databases (GeneCards, etc...) I can't find the same results and correspondance between the genes and the GO term that I found with "org.Hs.eg.db".

Do you know a better way? Am I missing something here?

Thanks

Answer 1

[Pierre Lindenbaum]

Not R. I wrote http://lindenb.github.io/jvarkit/GoUtils.html

Use GO annotation to retrieve genes associated to GO:0005216 ‘ion channel activity’

join -t $'\t' -1 1 -2 2 \
    <(java -jar dist/goutils.jar -A 'GO:0005216' | cut -f 1 | sort | uniq) \
    <(wget -q -O - "http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD" | gunzip -c | grep -v '^!' | cut -f3,5 | uniq | LC_ALL=C sort -t $'\t' -k2,2) |\
sort -t $'\t' -k2,2 |\
grep SCN5A -A 10 -B 10
(...)
GO:0086006  SCN2B
GO:0005244  SCN3A
GO:0005248  SCN3A
GO:0005248  SCN3A
GO:0005248  SCN3B
GO:0086006  SCN3B
GO:0005248  SCN4A
GO:0005248  SCN4A
GO:0005248  SCN4B
GO:0086006  SCN4B
GO:0005244  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0086006  SCN5A
GO:0086060  SCN5A
GO:0086061  SCN5A
GO:0086062  SCN5A
GO:0086063  SCN5A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN8A
GO:0005248  SCN8A
GO:0005248  SCN9A
GO:0005248  SCN9A
GO:0005248  SCN9A
GO:0005272  SCNN1A
(...)

[Francois Piumi]

Thanks Pierre. But GO terms in the list are not GO:0005216, why? I would have expected to have only a list of genes corresponding to this GO term.

[Pierre Lindenbaum]

Thanks Pierre. But GO terms in the list are not GO:0005216, why?

because GO is a graph. All those GO-Ids are a children of GO:0005216 "ion channel activity"

e.g: "GO:0086061" is "voltage-gated sodium channel activity involved in bundle of His cell action potential"