[BioC] using biomaRt to find all genes with kinase activity (and perhaps a Gene Ontology question too)
huber at ebi.ac.uk
Tue Dec 16 19:15:35 CET 2008
Hi James, Andrew
to get all children of the GO term GO:0016301, you can use
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]])
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:
> 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[])
>> 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,
> 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
>> 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 =
>> 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
>> 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
>> with biomaRt?
>> Many thanks,
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