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 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 wrote: > >> On Fri, Jun 10, 2011 at 11:12 AM, Ed 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 >> wrote: >> >> >> >> > Try the Molecular Signatures Database maintained by the Broad >> Institute. >> >> > >> >> > On Thu, Jun 9, 2011 at 5:24 PM, Ed 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]]