Apologies, if this is a naive question, but I've been trying to use biomaRt
to retrieve all genes with kinase activity.

I use the GO term GO:0016301 as follows:

 ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
results <- getBM(c("entrezgene", "hgnc_symbol", "unigene"), filters = "go",
values = "GO:0016301"  , mart=ensembl)

This pulls the usual results, e.g. like EGFR.


However, it doesn't retrieve results for genes like ATM, which in Gene
Ontology, is listed as a child of the GO term

http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?gptype=all&speciesdb=all&taxid=9606&evcode=all&term_assocs=all&term=GO%3A0016301&session_id=7978amigo1229194926&action=filter

I would have thought that this query would retrieve genes listed with that
GO term and the associated children of the GO term.

On a follow up note, is there a filter by which I can just search "kinase"
with biomaRt?

Many thanks,
Andrew

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