Hi Serdar,
Please send any Ensembl data related queries to [email protected].
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
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
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