Hi List, I've got an Affy timecourse experiment with 8 timepoints and I'm interested in finding which transcription factors (TF) are controling the expression of a particular gene (hk1). I don't know if there's any tool in Bionconductor that might allow me to do this? Or is there a freely accessible database that will tell me which TFs are know to control this gene, or even a tool that could infer such a result. I though it might be useful to look at genes that have a strong correlation in expression profile with hk1 over the 8 timepoints and compare what TFs are common to all (or many) of those genes? But again I'm not sure if or where the TF information is available? Regards, Peter. -- Dr. Peter Smith Dept. of Biostatistics National University of Ireland Maynooth [[alternative HTML version deleted]]

Hi Peter, I wrote a package called rHVDM. It does not do quite what you want, but you might want to check it out. Basically if you know some targets of a transcription factor, It will deduce the activation profile of that transcription factor and then using this information, it will predict which other genes might be targets, all based on the kind of data you have. Multiple transcription dependency is in project (and subject of current research elsewhere too). HTH M. On 24 Apr 2009, at 16:28, Peter Smith wrote: > Hi List, > > I've got an Affy timecourse experiment with 8 timepoints and I'm > interested > in finding which transcription factors (TF) are controling the > expression of > a particular gene (hk1). > > I don't know if there's any tool in Bionconductor that might allow > me to do > this? Or is there a freely accessible database that will tell me > which TFs > are know to control this gene, or even a tool that could infer such a > result. > > I though it might be useful to look at genes that have a strong > correlation > in expression profile with hk1 over the 8 timepoints and compare > what TFs > are common to all (or many) of those genes? But again I'm not sure > if or > where the TF information is available? > > Regards, > > Peter. > > -- > Dr. Peter Smith > Dept. of Biostatistics > National University of Ireland > Maynooth > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor >