Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
1
0
Entering edit mode
10 months ago

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.

refseq_mrna_predicted biomaRt refseq XM • 508 views
ADD COMMENT
2
Entering edit mode
10 months ago
GenoMax 139k

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
ADD COMMENT
0
Entering edit mode

Thank you very much, this helps a lot!

ADD REPLY

Login before adding your answer.

Traffic: 2259 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6