org.Mm.eg.db UNIPROT missing values
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@juliechevalier-13173
Last seen 4.1 years ago

Hi,

I'm working with the latest version of AnnotationDbi(1.38.2) and org.Mm.eg.db (3.4.1) in R 3.3.3.

I've tried to retrieve matching SYMBOL with UNIPROT ID with this command :

select(org.Mm.eg.db,"P53784",column="SYMBOL",keytype="UNIPROT")

I've obtained this error :

Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'UNIPROT'. Please use the keys method to see a listing of valid arguments.

 

It seems that this UNIPROT (verified by printing all UNIPROT of org.Mm.eg.db with this command : keys(org.Mm.eg.db,keytype="UNIPROT") doesn't exist in the database while this UNIPROT ID exists for mouse and correspond to the "Sox3" gene.

When I try the same command with sox3 gene as entry, I obtain this result :

select(org.Mm.eg.db,"Sox3",column="UNIPROT",keytype="SYMBOL")
'select()' returned 1:many mapping between keys and columns
  SYMBOL UNIPROT
1   Sox3  A2AM37
2   Sox3  Q5RKW0

The status of these two UNIPROT ID is "unreviewed" inthe UNIPROTKB website while the uniprot P53784 is "reviewed" but not contained in the DB!

I have the same problem with several UNIPROT ID, is it normal ? is there an other version of the database containing all UNIPROT ID ?

Thanks in advance

Julie

 

Annotation mouse UNIPROT • 741 views
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Mike Smith ★ 5.2k
@mike-smith
Last seen 14 hours ago
EMBL Heidelberg / de.NBI

If you take a look at the manual pages for org.Mm.eg.db it gives the following details on how the Uniprot mappings are derived: 

"This object is a simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to Uniprot Accession Numbers"

So we can take a look at the NCBI entry for Sox-3 at https://www.ncbi.nlm.nih.gov/gene/20675 to try and understand a little more.

If you jump to the RefSeq section of that page (here) you'll see two values listed next to UniProtKB/TrEMBL: A2AM37 & Q5RKW0.  There are the two reported in the package.

P53784 is mentioned further down the pages as a "related sequence".  This doesn't necessarily answer the question as to which mapping you want to use, but it at least explains why you find the discrepancy in org.Mm.eg.db

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