[BioC] biomaRt: how to retrieve the MOUSE gene symbol?

[James W. MacDonald]

Hi Guido,

Hooiveld, Guido wrote:
> Dear list,
> 
> Likely an easy question, but can someone plz inform me how to
> retrieve the MOUSE gene symbol using biomaRt? For human you can use
> as attribute "hgnc_symbol", and for mouse genes I also would like to
> have the gene symbol returned. I do know this property is present at
> Ensembl as MGI Symbol, but when listing the filters for Mouse I don't
> find this entry.

 > getBM("markersymbol", "affy_mouse430_2", "1415670_at", mart)
   markersymbol
1         Copg

Best,

Jim


> 
> Thanks, Guido
> 
> My code: [Note: I do know why I get the error; that's because I am
> querying mouse and not human, and the attribute hgnc_symbol does not
> exist in mmusculus_gene_ensembl. The question is which attribute to
> use for mouse?].
> 
> 
>> library(biomaRt)
> Loading required package: XML Loading required package: RCurl Warning
> message: package 'biomaRt' was built under R version 2.6.0
>> ensembl = useMart("ensembl") ensembl =
>> useDataset("mmusculus_gene_ensembl",mart=ensembl)
> Checking attributes and filters ... ok
>> # to check which information is available that can be retrieved: 
>> filters = listFilters(ensembl) filters
> name                              description 1
> affy_mg_u74a                       Affy mg u74a ID(s) 2
> affy_mg_u74av2                     Affy mg u74av2 ID(s) 3
> affy_mg_u74b                       Affy mg u74b ID(s) 4
> affy_mg_u74bv2                     Affy mg u74bv2 ID(s) Etc. <snip>
> by me
>> e <- getBM(attributes=c("uniprot_swissprot_accession",
>> "uniprot_swissprot", "hgnc_symbol", "entrezgene",
>> "ensembl_transcript_id"),  filter="uniprot_swissprot_accession",
>> values=swissprot_ids, mart=ensembl)
> Error in getBM(attributes = c("uniprot_swissprot_accession",
> "uniprot_swissprot",  : Invalid attribute(s): hgnc_symbol Please use
> the function 'listAttributes' to get valid attribute names
>> sessionInfo()
> R version 2.5.0 (2007-04-23) i386-pc-mingw32
> 
> locale: LC_COLLATE=English_United
> Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> 
> attached base packages: [1] "stats"     "graphics"  "grDevices"
> "utils"     "datasets"  "methods" [7] "base"
> 
> other attached packages: biomaRt    RCurl      XML "1.11.3"  "0.8-0"
> "1.7-3"
> 
> 
> 
> 
> ------------------------------------------------ Guido Hooiveld, PhD 
> Nutrition, Metabolism & Genomics Group Division of Human Nutrition 
> Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen 
> the Netherlands
> 
> tel: (+)31 317 485788 fax: (+)31 317 483342
> 
> internet:   http://nutrigene.4t.com email:      guido.hooiveld at wur.nl
> 
> 
> 
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> 
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