[BioMart Users] Retrieving promoter sequences of human genes

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[BioMart Users] Retrieving promoter sequences of human genes

Bozdag, Serdar (NIH/NCI) [F]
Hi

I would like to retrieve promoter sequences of a list of human genes in Biomart. I have the HUGO gene symbols for these genes. I do the necessary configurations in biomart but could not retrieve sequence for all genes. Would you let me know if I am missing something?

Here is the details of my query:

I select Homo sapiens genes (GRCh37.p2) as my database.

Then I select "HGNC symbol(s) [e.g. ZFY]: [ID-list specified]" in the filtering and upload my gene list.

For attributes, I make following selections:

 Attributes
Ensembl Gene ID
Ensembl Transcript ID
Flank-coding region (Gene)
Upstream flank [300]
Associated Gene Name

I have about 6,000 genes in my list and I only get promoter sequence for about 4,000 of them.

What could be the problem?

Thanks,

Serdar
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Re: [BioMart Users] Retrieving promoter sequences of human genes

Rhoda Kinsella
Hi Serdar,
Please send any Ensembl data related queries to [hidden email].  
It may also be useful if you send your gene list to the helpdesk team  
as this will help them to track down any issues.
Regards
Rhoda

On 3 Mar 2011, at 16:22, Bozdag, Serdar (NIH/NCI) [F] wrote:

> Hi
>
> I would like to retrieve promoter sequences of a list of human genes  
> in Biomart. I have the HUGO gene symbols for these genes. I do the  
> necessary configurations in biomart but could not retrieve sequence  
> for all genes. Would you let me know if I am missing something?
>
> Here is the details of my query:
>
> I select Homo sapiens genes (GRCh37.p2) as my database.
>
> Then I select "HGNC symbol(s) [e.g. ZFY]: [ID-list specified]" in  
> the filtering and upload my gene list.
>
> For attributes, I make following selections:
>
> Attributes
> Ensembl Gene ID
> Ensembl Transcript ID
> Flank-coding region (Gene)
> Upstream flank [300]
> Associated Gene Name
>
> I have about 6,000 genes in my list and I only get promoter sequence  
> for about 4,000 of them.
>
> What could be the problem?
>
> Thanks,
>
> Serdar
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users

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

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