
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.

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@wur.nl


	[[alternative HTML version deleted]]

