Thanks for the suggestion!

Andrew


On 12/13/08, James W. MacDonald <jmacdon@med.umich.edu> wrote:
>
> Hi Andrew,
>
> 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:
>
> > library(org.Hs.eg.db)
> Loading required package: AnnotationDbi
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: DBI
> > all.egs <- mget("GO:0016301", org.Hs.egGO2ALLEGS)
> > all.egs <- unique(all.egs[[1]])
> > 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=","))
> > head(all.dat)
>   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
> > dim(all.dat)
> [1] 796   3
>
>
> Best,
>
> Jim
>
>
>
>
> 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
>>
>>
>> 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
>>
>>        [[alternative HTML version deleted]]
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-5646
> 734-936-8662
>

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