Hi i have some transcript id like ENSCAFT00000059187.1 ENSCAFT00000059235.1 ENSCAFT00000059242.1 ENSCAFT00000059247.1 how can i get the gene symbol from these ids......
thanks in advances
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mahfuz.290066 •
Ensembl BioMart instructions might help you: http://www.ensembl.org/Help/Faq?id=125
The four example genes you posted are lincRNAs that don't yet have gene IDs. In general, you can do what Alex Reynolds suggested and use Ensembl biomart.
As an aside, the "URL" function on Ensembl biomart doesn't seem to work at the moment (otherwise I would have linked to the results). I've reported the issue.
In R, for mapping ensembl transcript IDs to ensembl gene ID and gene symbol: 1) Install EnsDb.Hsapiens.v86 2) Run following command for a transcript in TP53 gene: select(EnsDb.Hsapiens.v86, columns = c("ENTREZID","GENEID", "GENENAME"), keytype = "TXID", keys=c("ENST00000617185"))
However, your transcripts are non coding RNAs and belongs to dog (C.fa). They may not have gene IDs mapped (in ensembl). (as mentioned abvoe) in EnsDb.
g: Profiler will be quite useful for Gene ID conversion. This might work out for you.
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More details will be easy to give some solution. What is your organism (assuming dog) and how did you get those ids ?