This would depend on whether you have access to annotations listing coordinates of binding sites. I am not sure whether these are accessible from the UCSC. Jennifer -> can you point Charlie to this bright direction here.
Thanks,
anton galaxy team
On Oct 29, 2010, at 10:50 AM, CCT Hindmarch, Henry Wellcome Laboratories Integrated Neuroscienc wrote:
Dear Anton,
Thanks for the reply, my gene lists actually come with coordinates already. I know how to compare and get 1kb upstream of these genes. What I am not sure what to do is identify whether these genes have promotors for a particular transcription factor... i.e. which of the regulated genes from my array have a particular transcription factor binding site in their promotor region. I would like to be able to present lists of AP1 responsive genes, CREB responsive genes, etc etc...
All the best, and thank you in advance for all your assistance
Charlie
--On Friday, October 29, 2010 10:37 -0400 Anton Nekrutenko anton@bx.psu.edu wrote:
Chipboy101:
There is a VERY old screencast (Galaxy looked different back in 2008 and the screencast is non streamable) that you can download from here (~a 15 Mb file):
http://screencast.g2.bx.psu.edu/old/geneNames.mov
it is a quicktime movie. This should get you on the right track in terms of going from gene names to genomic coordinates.
Let us know if you have problems.
anton galaxy team
On Oct 29, 2010, at 10:16 AM, CCT Hindmarch, Henry Wellcome Laboratories Integrated Neuroscienc wrote:
Hi,
I am playing with Galaxy ahead of getting ChipSeq data and it looks brilliant (thanks)...
I wonder whether It is possible to input a list of genes from a standard microarray experiment, identify the promotor regions of each gene and then work out which Transcription factor binding sites are contained in this gene list? Maybe a silly question, but this would be very useful information for me...
All the best
Charlie (chipboy101)
Dr CCT Hindmarch Henry Wellcome Laboratories Integrated Neuroscience and Endocrinology _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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Dr CCT Hindmarch Henry Wellcome Laboratories Integrated Neuroscience and Endocrinology
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org