[BioC] TF database

[Sean Davis]

On Fri, Jun 10, 2011 at 11:12 AM, Ed <edforum at gmail.com> wrote:
> Sure. Thanks.
>
> A less related question again :)
>
> If I would like to build a pathway between any two proteins, like from a
> receptor to a TF or from a kinase to a TF, which is the best way to get it.
> I do not need a graph but a n-step "noodle"?

You'll probably need to define "pathway" here.  More specifically,
you'll need to define for yourself what constitutes a "link" between
two proteins.  You might consider looking at pathway databases as a
first approximation, though.

Sean

> If it is a bit off-topic for bioconductor, I apologize.
>
> Thanks again,
>
> Ed
>
>
>
> On Fri, Jun 10, 2011 at 3:47 AM, Sole Acha, Xavi <x.sole at iconcologia.net>wrote:
>
>> Hi Ed,
>>
>> You can use Gene Ontology database, and get the gene products under the
>> terms "Regulation of transcription", "Transcription regulator activity" and
>> "Nucleic acid binding transcription factor activity" (some other GO terms
>> may apply for you).
>>
>> Besides, for a recent paper describing a list of curated TFs have a look
>> at:
>>
>> http://www.ncbi.nlm.nih.gov/pubmed?term=19274049
>>
>> Best,
>>
>> Xavi.
>>
>> ------
>> Xavier Solé Acha
>> Unitat de Biomarcadors i Susceptibilitat
>> Unit of Biomarkers and Susceptibility
>> Institut Català d'Oncologia // Catalan Institute of Oncology
>> Gran Via de L'Hospitalet 199-203
>> 08908 L'Hospitalet de Llobregat, Barcelona, Spain.
>> Phone: +34 93 260 71 22 / +34 93 260 71 86 (ext. 7122)
>> Fax: +34 93 260 71 88
>> E-mail: x.sole (at) iconcologia.net
>>
>>
>> -----Mensaje original-----
>> De: bioconductor-bounces at r-project.org [mailto:
>> bioconductor-bounces at r-project.org] En nombre de Ed
>> Enviado el: viernes, 10 de junio de 2011 1:22
>> Para: Michael Gormley
>> CC: bioconductor at r-project.org
>> Asunto: Re: [BioC] TF database
>>
>> Thanks. I forgot C3 itself is.
>>
>> Any bigger or other options?
>>
>>
>>
>> On Thu, Jun 9, 2011 at 4:59 PM, Michael Gormley <mpg33 at drexel.edu> wrote:
>>
>> > Try the Molecular Signatures Database maintained by the Broad Institute.
>> >
>> > On Thu, Jun 9, 2011 at 5:24 PM, Ed <edforum at gmail.com> wrote:
>> >
>> >> Hi there,
>> >>
>> >> Is there a good TF database or table that can be imported to
>> bioconductor?
>> >> Or direct downloading is ok too.
>> >>
>> >> I tried Transfac but it only provides a web-access search instead of a
>> >> table? I need to know the TF id with its regulating genes.
>> >>
>> >> Thanks,
>> >>
>> >> Ed
>> >>
>> >>        [[alternative HTML version deleted]]
>> >>
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>> >
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