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how to obtain the locations of a exon and its corresponding peptide from a specific transcript in bioMart

I tried to connect a transcript (ENSTxxx)'s exons to their corresponding peptides (residues) using bioMart in R.

library("biomaRt")
ensembl<- useMart("ensembl")
ensembl<- useDataset( "ensembl", dataset="hsapiens_gene_ensembl")
getBM(c('peptide_location','exon_chrom_start','exon_chrom_end'), filters = c('ensembl_transcript_id','pdb'), values=list('ENST00000606293','2ZA5'), mart=ensembl)
Error in getBM(c("peptide_location", "exon_chrom_start", "exon_chrom_end"),  :
  Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed

I wish to get some help for this problem.

peptide biomart exon
• 4,223 views • link
updated by Ram Ram • written by jjaeyun • jjaeyun

1 answer

This has to do with the way the Biomart webserver/database is set up. Essentially, you can't do gene-based queries and transcript-based queries at one time. But you can do them sequentially and merge at the end.

transcript_data<-getBM(c('ensembl_transcript_id','exon_chrom_start','exon_chrom_end'), filters = c('ensembl_transcript_id','pdb'), values=list('ENST00000606293','2ZA5'), mart=ensembl)
pept_data<-getBM(c('ensembl_transcript_id','peptide_location'), filters = c('ensembl_transcript_id','pdb'), values=list('ENST00000606293','2ZA5'), mart=ensembl)
final_data<-merge(transcript_data, pept_data, by='ensembl_transcript_id')
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updated by Ram Ram • written by informatics bot informatics bot

Thank you so much! It worked. And, it answers for my rest of work. Thanks again!

BTW, this was my first use of Biostart. This is pretty nice

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written by jjaeyun • jjaeyun

You're very welcome :D

feel free to up-vote my "answer" and mark this question as solved.

• 0 views • link
written by informatics bot informatics bot

Hi Lando,

I thought your code was what I wanted, but actually, it is not.

In your merge function at the end, it was supposed to be exon range or exon id, other than transcript id. Could you correct this?

Thanks,

• 0 views • link
updated by Ram Ram • written by jjaeyun • jjaeyun

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