from names(jaspar) there are only 22 gene symbols of TFs overlapped with c3 from broad. Any suggestion? Ed On Fri, Jun 10, 2011 at 1:02 PM, Hollis Wright <wrighth@ohsu.edu> wrote: > 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@r-project.org [ > bioconductor-bounces@r-project.org] On Behalf Of Ed [edforum@gmail.com] > Sent: Friday, June 10, 2011 10:59 AM > To: Sean Davis > Cc: bioconductor@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@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@mail.nih.gov> > wrote: > > > >> On Fri, Jun 10, 2011 at 11:12 AM, Ed <edforum@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@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@r-project.org [mailto: > >> >> bioconductor-bounces@r-project.org] En nombre de Ed > >> >> Enviado el: viernes, 10 de junio de 2011 1:22 > >> >> Para: Michael Gormley > >> >> CC: bioconductor@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@drexel.edu> > >> wrote: > >> >> > >> >> > Try the Molecular Signatures Database maintained by the Broad > >> Institute. > >> >> > > >> >> > On Thu, Jun 9, 2011 at 5:24 PM, Ed <edforum@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]] > >> >> >> > >> >> >> _______________________________________________ > >> >> >> Bioconductor mailing list > >> >> >> Bioconductor@r-project.org > >> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> >> Search the archives: > >> >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> >> > >> >> > > >> >> > > >> >> > >> >> [[alternative HTML version deleted]] > >> >> > >> >> _______________________________________________ > >> >> Bioconductor mailing list > >> >> Bioconductor@r-project.org > >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> Search the archives: > >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> > >> >> _______________________________________________ > >> >> Bioconductor mailing list > >> >> Bioconductor@r-project.org > >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> Search the archives: > >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor@r-project.org > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > >> > > > > > > [[alternative HTML version deleted]] > > [[alternative HTML version deleted]]