Ensembl Transcript Id's to Gene Names for Rabbit (Oryctolagus cuniculus)

Hello Biostars community,

My Data have transcript ids for rabbit (Oryctolagus cuniculus, Release 93, OryCun2.0) and I am trying to find out their corresponding gene names. I have tried ftp servers of Ensembl to extract gene names and transcript ids but, unable to autonomously obtain data.

Transcript_ID   
ENSOCUT00000001776  
ENSOCUT00000001777
ENSOCUT00000001779  
ENSOCUT00000001780  
ENSOCUT00000001781  
ENSOCUT00000001782  
ENSOCUT00000001783
ENSOCUT00000XXXXXX

Desired format is like this;

Transcript_ID      Gene_Name
ENSOCUT00000001776  REST
ENSOCUT00000001777  GOSR1
ENSOCUT00000001779  ZDHHC9
ENSOCUT00000001780  BHLHA9
ENSOCUT00000001781  PREX2
ENSOCUT00000001782  BCL7B
ENSOCUT00000001783  TBL2
ENSOCUT00000XXXXXX  YYYY

Can you guide me about how to extract corresponding gene names of the transcripts of rabbit ?

rna-seq ensembl rabbit

• 2,573 views • link

updated 7.9 years ago by jared.andrews07

• written 7.9 years ago by rekren •

Please follow Alastair Kerr's solution from this post: Ensembl Ids To Gene Name Conversion

Use Biomart from the Ensembl site. 'Filter' your query based on your Ensembl ids make sure the Gene name is checked under the 'Attributes'.

• 1 views • link

written 7.9 years ago by Sej Modha

Thank you so much Sej.

• 1 views • link

written 7.9 years ago by rekren •

1 answer

This can be done with biomart in R.

library("biomaRt")
ensembl = useMart("ensembl",dataset="ocuniculus_gene_ensembl")

# Test a few of them.
your_transcript_ids <- c("ENSOCUT00000001776","ENSOCUT00000001779")

annotations <- getBM(attributes=c('ensembl_transcript_id', 'hgnc_symbol'), 
      filters = 'ensembl_transcript_id', 
      values = your_transcript_ids, 
      mart = ensembl)

Results in:

  ensembl_transcript_id hgnc_symbol
1    ENSOCUT00000001776        REST
2    ENSOCUT00000001779      BHLHA9

I don't know if you copy/pasted the symbol for the second one wrong or just threw in some example symbols to show what you want, but this should get you most of the way there.

• 1 views • link

written 7.9 years ago by jared.andrews07

Thanks a lot for your well structured answer Jared, I have just threw random gene names as an example.

• 1 views • link

written 7.9 years ago by rekren •