Question: Missing ensembl_ids in biomaRt uniprot query
0
gravatar for António Miguel de Jesus Domingues
4.9 years ago by
Germany

I am trying to do a "classical" match of uniprot ids, using protein IDs identified in a Zebrafish mass-spec experiment, to find the corresponding ensembl gene ids. However, there are several proteins for which my biomaRt query fails to retrive any information, although they are present in the Uniprot database and with an attributed ensembl gene id. Am I missing something?

 

Here is my code:

prot_ids = c("F1QCB4", "F1R8H7", "A0JMF6", "F1QU18", "A0JMK7", "A0MTA1")

uniProt <- useMart("unimart", dataset="uniprot")

getBM(
        attributes =c("accession" ,"name","ensembl_id", "gene_name"),
        filter="accession",
        values=prot_ids,
        mart=uniProt)

[1] accession  name       ensembl_id gene_name
<0 rows> (or 0-length row.names)

 

sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] biomaRt_2.22.0     VennDiagram_1.6.9  RColorBrewer_1.1-2

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1
 [4] bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.3  
 [7] IRanges_2.0.0        parallel_3.1.2       RCurl_1.95-4.5      
[10] RSQLite_1.0.0        S4Vectors_0.4.0      stats4_3.1.2        
[13] tcltk_3.1.2          tools_3.1.2          XML_3.98-1.1 
biomart ensembl uniprot • 726 views
ADD COMMENTlink modified 4.9 years ago by me0 • written 4.9 years ago by António Miguel de Jesus Domingues470
Answer: Missing ensembl_ids in biomaRt uniprot query
0
gravatar for me
4.9 years ago by
me0
European Union
me0 wrote:

Some of the accessions you are trying to map have been deleted from UniProt e.g. F1QCB4 your code should return results with the for example the accession P05067. However, it is likely that you will need to rerun the protein ACC mapping to using the Zebrafish mass-spec results.

 

See this example from the Biomart that shows the basic query is correct but no value exists for F1QCB4.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by me0

Yes, some correspond to deleted entries, but I do not understand what you mean with "rerun the protein ACC mapping to using the Zebrafish mass-spec results". Could you please explain in more detail?

ADD REPLYlink written 4.9 years ago by António Miguel de Jesus Domingues470
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