Retrieve hgnc_symbol from XM_ refseqs using BiomaRt

Question

[ladina.hoesli]

I have some predicted RefSeqs, such as XM_005261067 or XM_005255527 and would like to retrieve the hgnc_symbol using BiomaRt like this:

refseqids_XM = c("XM_005261067","XM_005255527")
gene_XM <- getBM(attributes=c("refseq_mrna_predicted","hgnc_symbol"), 
             filters="refseq_mrna_predicted",
             values=refseqids_XM, 
             mart=ensembl)
gene_XM

However, this gives me no result:

[1] refseq_mrna_predicted refseq_mrna          
<0 Zeilen> (oder row.names mit Länge 0)

I am not sure, but maybe these XM RefSeqs are too old and were removed from the dataset? Unfortunately, this is what I have to work with, as this is returned from our analysis pipline. Any idea on how I could still retrieve information using these XM RefSeqs would be highly appreciated.

Answer 1

[GenoMax]

maybe these XM RefSeqs are too old and were removed from the dataset?

These accessions appear to be deprecated so you may need to try an older version of Mart to see if you can get the information from there.

If you have a few ID's then Entrezdirect will give you a clue as to what they were:

$ esearch -db nuccore -query "XM_005255527.2" | esummary | xtract -pattern DocumentSummary -element Title
PREDICTED: Homo sapiens tuberous sclerosis 2 (TSC2), transcript variant X1, mRNA

$ esearch -db nuccore -query "XM_005261067" | esummary | xtract -pattern DocumentSummary -element Title
PREDICTED: Homo sapiens runt-related transcription factor 1 (RUNX1), transcript variant X1, mRNA

[ladina.hoesli]

Thank you very much, this helps a lot!