[BioC] using biomaRt to find all genes with kinase activity (and perhaps a Gene Ontology question too)

[Wolfgang Huber]

Hi James, Andrew

to get all children of the GO term GO:0016301, you can use

 library("GO.db")
 ch = GOMFCHILDREN[["GO:0016301"]]


You can supply that in the 'values' argument of your call to getBM.
To see what they are, use e.g.

 lapply(ch, function(x) GOTERM[[x]])

	Best wishes
	Wolfgang


------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber



13/12/2008 21:35 James W. MacDonald scripsit
> 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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>