On Wed, Jul 29, 2009 at 3:35 AM, <mauede@alice.it> wrote:

>  Actually I extracted the same information the old way, that is using a
> loop which provided one refseq_dna at a time.
> I know thsi is not expected with a high-level language like R. However i
> could see that some ENST correspond to two different
> HGNC symbols. Moreover the 3utr sequence is not available for all ENSTs I
> have.
>
Not all transcripts have a 3'utr.  If you want to check your code, you can
always go to the Ensembl browser to see what it shows for those transcripts
for which the 3'utr is missing.

Sean


>
> Thank you for your answer.
> Regards,
> Maura
>
>
> -----Messaggio originale-----
> Da: Sean Davis [mailto:seandavi@gmail.com <seandavi@gmail.com>]
> Inviato: mer 29/07/2009 7.46
> A: mauede@alice.it
> Cc: Bioconductor List
> Oggetto: Re: [BioC] Why am I finding a mismatch between refseq_dna and
> ensembl_transcript_id ?
>
> On Wed, Jul 29, 2009 at 12:01 AM, <mauede@alice.it> wrote:
>
> > I downloaded the following file from miRDB
> > http://mirdb.org/miRDB/download/MirTarget2_v3.0_prediction_result.txt.gz
> >
> > I have checked that miRDB Gene_Bank_Accession_Number (for Human it is
> > something like NM_xxxxx) correspond to BioMart "refseq_dna".
> >
> > I have a vector containing 253  Gene_Bank_Accession_Numbers
> >  length(tmp_miRNA_GB)
> > [1] 253
> > > tmp_miRNA_GB[1:5]
> > [1] "NM_203390"    "NM_024639"    "NM_001017989" "NM_203331"
> "NM_001879"
> >
> > I use such a vectos as input filter to getBM to obtain the respective
> > ensembl_transcript_id.
> > Surprisingly onlly 246 ensembl_transcript_ids are found:
> >
> > > gene.map <- getBM (attributes =
> > c("hgnc_symbol","ensembl_gene_id","refseq_dna","ensembl_transcript_id"),
> >                                       filters = "refseq_dna", values =
> > tmp_miRNA_GB, mart=hmart)
> >
> > > dim(gene.map)
> > [1] 246   4
> >
> > I thought there would be a 1-1 correspondence between the two attributes:
> > "refseq_dna" and "ensembl_transcript_id"
> > Am I mistaken ?
> >
>
> Hi, Maura.
>
> Yes, unfortunately, there is not a 1-1 correspondence.  Ensembl and NCBI
> (the curator of RefSeq) are independent organizations, each with different
> build policies and annotation processes for transcripts.  So, in general in
> this field (genomics/bioinformatics), there is RARELY a 1-1 correspondence
> between any two entities.  I would suggest that 246/253 is actually quite a
> good result--I might have expected a bit less a priori.
>
> Sean
>
>
>
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