[BioC] using biomaRt to find all genes with kinase activity (and perhaps a Gene Ontology question too)
James W. MacDonald
jmacdon at med.umich.edu
Sat Dec 13 22:35:28 CET 2008
I don't know if you can get all the children from biomaRt, but you can
get them from the org.Hs.eg.db package:
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Loading required package: DBI
> all.egs <- mget("GO:0016301", org.Hs.egGO2ALLEGS)
> all.egs <- unique(all.egs[])
> all.dat <- data.frame("Entrez Gene" = all.egs, "Symbol" =
unlist(mget(all.egs, org.Hs.egSYMBOL, ifnotfound=NA)), "UniGene" =
sapply(mget(all.egs, org.Hs.egUNIGENE, ifnotfound=NA), paste, collapse=","))
Entrez.Gene Symbol UniGene
25 25 ABL1 Hs.431048
27 27 ABL2 Hs.159472
90 90 ACVR1 Hs.470316
91 91 ACVR1B Hs.438918
92 92 ACVR2A Hs.470174
93 93 ACVR2B Hs.174273
 796 3
Andrew Yee wrote:
> 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
> 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,
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James W. MacDonald, M.S.
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