[biomart-users] Extra lines in results with uniprot_swissprot_accession

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

[biomart-users] Extra lines in results with uniprot_swissprot_accession

Jose Zamalloa
Hi,

I just started using biomart and so far it is what I've looking for. I have a question regarding the output of results when going from:

filters="hgnc_symbol"

to:

attributes=c("hgnc_symbol", "uniprot_swissprot_accession")

I get some results (even in the web interface) that are duplicates of my query (hgnc_symbol) but contain no result record (uniprot_swissprot_accession), for example:

 hgnc_symbol uniprot_swissprot_accession
1       ALOX5                      P09917
2       ALOX5                           

I get the right UNIPROT for my gene of interest, but I also get another record with a blank space in the right column. Is there any reason for this?

Just for reference my code in R is:
ensembl=useMart("ensemble")
ensembl=useDataset(dataset="hsapiens_gene_ensembl",mart=ensembl)
GENES=read.table("GENES")
RESULTS=getBM(attributes=c("hgnc_symbol", "uniprot_swissprot_accession"), filters="hgnc_symbol", values=GENES[,1],
             mart=ensembl)

I get the same results when I do it through: http://useast.ensembl.org/biomart/martview/6d162917c8561a8ac078ebb20431f270

Thank you,
Jose

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at http://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/groups/opt_out.
 
 
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] Extra lines in results with uniprot_swissprot_accession

Rhoda Kinsella
Hi Jose
If you add the attributes Ensembl gene id and Ensembl transcript id, then this will help you to understand the reason for the empty UniProt result field (see image attached). Basically, the Ensembl gene mart is Ensembl gene centric. We map various external references sources, such as HGNC and UniProt, to our genes. As you will see from the result set in the image, this Ensembl gene has two transcripts, one of which has a UniProt SwissProt accession mapped to it and the other doesn't. I hope that helps. If you have any further Ensembl data questions, please email [hidden email].
Regards
Rhoda

On 20 Jul 2013, at 00:22, Jose Zamalloa <[hidden email]> wrote:

Hi,

I just started using biomart and so far it is what I've looking for. I have a question regarding the output of results when going from:

filters="hgnc_symbol"

to:

attributes=c("hgnc_symbol", "uniprot_swissprot_accession")

I get some results (even in the web interface) that are duplicates of my query (hgnc_symbol) but contain no result record (uniprot_swissprot_accession), for example:

 hgnc_symbol uniprot_swissprot_accession
1       ALOX5                      P09917
2       ALOX5                           

I get the right UNIPROT for my gene of interest, but I also get another record with a blank space in the right column. Is there any reason for this?

Just for reference my code in R is:
ensembl=useMart("ensemble")
ensembl=useDataset(dataset="hsapiens_gene_ensembl",mart=ensembl)
GENES=read.table("GENES")
RESULTS=getBM(attributes=c("hgnc_symbol", "uniprot_swissprot_accession"), filters="hgnc_symbol", values=GENES[,1],
             mart=ensembl)

I get the same results when I do it through: http://useast.ensembl.org/biomart/martview/6d162917c8561a8ac078ebb20431f270

Thank you,
Jose

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at http://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD



--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at http://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/groups/opt_out.
 
 
Reply | Threaded
Open this post in threaded view
|

[biomart-users] Re: Extra lines in results with uniprot_swissprot_accession

Jose Zamalloa
In reply to this post by Jose Zamalloa
Thanks Rhoda! That was really helpful!

Jose

On Friday, July 19, 2013 7:22:05 PM UTC-4, Jose Zamalloa wrote:
Hi,

I just started using biomart and so far it is what I've looking for. I have a question regarding the output of results when going from:

filters="hgnc_symbol"

to:

attributes=c("hgnc_symbol", "uniprot_swissprot_accession")

I get some results (even in the web interface) that are duplicates of my query (hgnc_symbol) but contain no result record (uniprot_swissprot_accession), for example:

 hgnc_symbol uniprot_swissprot_accession
1       ALOX5                      P09917
2       ALOX5                           

I get the right UNIPROT for my gene of interest, but I also get another record with a blank space in the right column. Is there any reason for this?

Just for reference my code in R is:
ensembl=useMart("ensemble")
ensembl=useDataset(dataset="hsapiens_gene_ensembl",mart=ensembl)
GENES=read.table("GENES")
RESULTS=getBM(attributes=c("hgnc_symbol", "uniprot_swissprot_accession"), filters="hgnc_symbol", values=GENES[,1],
             mart=ensembl)

I get the same results when I do it through: http://useast.ensembl.org/biomart/martview/6d162917c8561a8ac078ebb20431f270

Thank you,
Jose

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at http://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/groups/opt_out.