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

Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

---------------------- Dr CCT Hindmarch Henry Wellcome Laboratories Integrated Neuroscience and Endocrinology

Hi Charlie - The most TF track options at UCSC are in the database labeled hg18 (Human Mar. 2006 NCBI36). If you are using another genome, the same general rules here would apply - just look in the "Regulation" track group for the available choices (if any). http://genome.ucsc.edu -> Genome Browser -> hg18 In hg18, the usual favorite is "TFBS Conserved". See the track's description for the methods. The quality of this particular dataset is considered to be very good by many scientists working with TFs. Other suggested tracks with direct TF mappings are: ORegAnno, SwitchGear TSS, 7X Reg Potential. Once you decide on a track (or set of tracks to experiment with), use "Get Data" to pull the data over in BED/interval format from the Table browser and compare using Galaxy vs your dataset's predicted promoter regions (that are also in interval format). Sourcing from Bx Main (a mirror) will be faster than using UCSC Main and would be required for the very large tables. In the hg18 Regulation track group, you will also find tracks sourced from ENCODE. This mainly signal-based data and some non-trivial filtering would be necessary to do the data reduction to identify discrete regions that meet "significant signal" criteria (sometimes per TF/TF group). Galaxy would actually be very good for this type of project since it would all be web-based with the testing/tuning analysis cycles saved easily into histories, workflows, and data libraries. If you have a question about an individual ENCODE track, the UCSC help mailing list would be the best place to get the most current info: genome@soe.ucsc.edu Hopefully this helps to get you started! Best, Jen Galaxy team On 10/29/10 7:54 AM, Anton Nekrutenko wrote:

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

Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

---------------------- Dr CCT Hindmarch Henry Wellcome Laboratories Integrated Neuroscience and Endocrinology

Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

-- Jennifer Jackson http://usegalaxy.org