[BioC] TF database

[Hollis Wright]

In general, JASPAR should be very high-quality as far as PWM-based sources go; the point of the JASPAR project was to be manually curated as far as is possible as well as to be open source. Can't speak to other sources, however. 

Hollis Wright, PhD
Knight Cancer Center
Oregon Health and Science University
________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Ed [edforum at gmail.com]
Sent: Friday, June 10, 2011 10:59 AM
To: Sean Davis
Cc: bioconductor at r-project.org
Subject: Re: [BioC] TF database

I searched and got a set of databases including JASPAR; but did not realize
the talk b/w it with bioconductor packages. Thanks.

I also would like to know about the quality of those databases.

Ed


On Fri, Jun 10, 2011 at 10:43 AM, Ed <edforum at gmail.com> wrote:

> The pathway or path here means a signal transduction from protein A to B,
> which makes the biological meaning..
>
> The pathway database usually takes form of gene set. I might need a PPI
> database.
>
> The key part is how to integrate them to serve my purpose. I am asking any
> suggestion on those databases so I can give a try.
>
> Thanks,
>
> Ed
>
>
> On Fri, Jun 10, 2011 at 10:18 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> 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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