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CCT Hindmarch, Henry Wellcome Laboratories Integrated Neuroscienc
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
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Re: (no subject)

Anton Nekrutenko
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):


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
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-user



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Re: (no subject)

CCT Hindmarch, Henry Wellcome Laboratories Integrated Neuroscienc
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
<[hidden email]> 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
> [hidden email]
> 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
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Re: (no subject)

Anton Nekrutenko
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 <[hidden email]> 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
>> [hidden email]
>> 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




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Re: (no subject)

Jen Hillman-Jackson
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:
[hidden email]

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<[hidden email]>  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
>>> [hidden email]
>>> 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
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Jennifer Hillman-Jackson
http://galaxyproject.org