Question: Genes associated with GO term
1
gravatar for mforde84
18 months ago by
mforde841.2k
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:

library(biomaRt)
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
gene.data <- 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 www.ebi.ac.uk. 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 • 944 views
ADD COMMENTlink modified 18 months ago by EagleEye5.6k • written 18 months 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:

library(org.Hs.eg.db)
gene_list <- data.frame(mget("GO:0072599", org.Hs.egGO2ALLEGS)[[1]])
ADD REPLYlink written 18 months ago by mforde841.2k
1
gravatar for EagleEye
18 months ago by
EagleEye5.6k
Sweden
EagleEye5.6k 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 18 months ago • written 18 months ago by EagleEye5.6k

great thats very helpful

ADD REPLYlink written 18 months ago by mforde841.2k
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