[BioC] predicting transcription factors

[Jing Huang]

Hi Paul,

Your interpretations are right on my problem.

Jing

On 6/5/12 10:24 AM, "Paul Shannon" <pshannon at fhcrc.org> wrote:

>Dear Jing Huang,
>
>Let me make sure I correctly grasp your problem.
>
> 1) You have a set of co-regulated genes
> 2) You wish to identify possible shared transcription factors for these
>genes
>
>If this is an accurate statement, then one good approach is to
> 
> 1) Obtain promoter sequence of each gene, often estimated to be 3k
>upstream, and 300 bases downstream, of the transcription start site.
>    BioC provides excellent tools and data for this.
>
> 2) Search for enriched transcription factor binding sites in these
>promoters.
>
>The meme website (or the downloaded meme software) is one traditional way
>to do the search.  We have some BioC packages, including MotIV, and my
>soon-to-be-released collection of transcription factor matrices, which
>provide a good solution for this also, and have the advantage that your
>analysis can be performed entirely in R, reproducibly.
>
>Is this helpful?  I can provide more detail.
>
> - Paul
>
>
>
>On Jun 5, 2012, at 9:44 AM, Jing Huang wrote:
>
>> Hi Experts,
>> 
>> I am interested in predicting transcription factors for a specific
>>family of genes. According to my readings, it is possible to predict
>>transcription factors for the genes that are expressed accordingly with
>>similar pattern (up or down regulated). I don't know how.
>> 
>> Can somebody provide advices?
>> 
>> Many thanks
>> 
>> Jing Huang PhD
>> 
>> OHSU
>> 
>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>