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-   -   finding promoters using ensembl biomart (http://seqanswers.com/forums/showthread.php?t=25407)

narges 12-01-2012 06:24 AM

finding promoters using ensembl biomart
 
Hi,

I have found the upstream promoter of length 200 for some genes using Ensembl Biomart. But my supervisor asked me to find 10 promoter of each gene and to find any similarity between them. How can I find 10 promoter for one gene? For example should I just change the length of upstream Flank(gene) section in biomart?
But then ofcourse they have some exactly common regions.
Can any one help me how to do this?
Thank you

jiaco 12-01-2012 02:05 PM

Are you sure the supervisor did not mean 10 promoters for 1 gene but from 10 different organisms? Unless the gene of interest has 10 different TSSs, I do not understand the question unless it means to look for cross-species similarity.

narges 12-01-2012 04:53 PM

This is what he has asked : "Take at least 10 gene promoters of the top hits....."
I also was thinking it can not be meaningful :(

GenoMax 12-03-2012 05:16 AM

Quote:

Originally Posted by narges (Post 90545)
This is what he has asked : "Take at least 10 gene promoters of the top hits....."
I also was thinking it can not be meaningful :(

What kind of top hits is he referring to? Are these genes from a study that has resulted in a rank ordered list?

Maybe he wants you to find common motifs (binding sites) in the promoter regions of the top 10 genes from the gene list.


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