Question: Genes associated with GO term
gravatar for mforde84
3.5 years ago by
mforde841.2k wrote:

I've read in an older thread that to retrieve all of the gene names associated with a GO id you use the biomaRt package, eg:

ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") <- getBM(attributes=c('hgnc_symbol', 
    'ensembl_transcript_id', 'go_id'), filters = 'go_id', 
    values = 'GO:0072599', mart = ensembl)

However, I'm not sure this is actually a correct answer since it returns 1 gene annotation compared to the 109 reported on Is there a more nuanced interpretation of what this one gene is? Is it only genes directly related to the term and no child terms? If so, is it appropriate to retrieve all child terms for the purpose of functional enrichment analysis, or to just use the 1 gene directly related to the term?

go gene • 2.1k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 3.5 years ago by mforde841.2k

It looks like it's just the genes that are directly related to the term, and no child terms. In order to get those I had to use:

gene_list <- data.frame(mget("GO:0072599", org.Hs.egGO2ALLEGS)[[1]])
ADD REPLYlink written 3.5 years ago by mforde841.2k

When I do this code

gene_list <- data.frame(mget("GO:0072599", org.Hs.egGO2ALLEGS)[[1]])

I get back a list of just numbers, not ensembl IDs. Any idea what these are or how to convert to ensembl?

ADD REPLYlink written 7 weeks ago by MaxF70
gravatar for EagleEye
3.5 years ago by
EagleEye6.6k wrote:

Hi, there is one more simple solution with GeneSCF. You can download all GO terms with associated Genes as tab-separated text file using simple command line. See this example.

In your case for Homo sapiens, use

./prepare_database -db=GO_all -org=goa_human

prepare_database usage

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by EagleEye6.6k

great thats very helpful

ADD REPLYlink written 3.5 years ago by mforde841.2k
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