Getting genes list associated to current GO terms
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Stane ▴ 40
@stane-10974
Last seen 6.2 years ago

Hi, I have been trying to retrieve a list of genes associated with a particular GO terms in R 

Using Biomart with the homo sapiens ensembl dataset I am getting a subset of the gene list from the website http://amigo.geneontology.org/

go_list_cell_cycle <- getBM(attributes=c('hgnc_symbol', 'go_id'),
                   filters = 'go_id', values = 'GO:0007049', mart = ensembl)

I was wondering if there were better solutions usable directly from R, otherwise, I will just manually save the data from the website. 

Best

 

 

biomart go • 1.3k views
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very good indeed, the genes seem to be all present with your package, thank you ! 

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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia

See How to get genes within a GO category of 'GOstat' results?

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