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

[James W. MacDonald]

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
> 
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> 
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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