This passed under my radar, sorry to intervene so late in the thread. I wrote a package that does just that, it's called rHVDM and downloadable from the Bioconductor website. It uses mechanistic models to predict targets of transcription factors, all is needed is a handful of known targets. The relevant paper is here: http:// www.ncbi.nlm.nih.gov/sites/entrez? cmd=Retrieve&db=PubMed&list_uids=16584535&dopt=AbstractPlus&holding=f1 00 0%2Cf1000m%2Cisrctn. OK, end of shameless self-promotion, but any questions and enquiries are more than welcome. Martino On 9 Aug 2007, at 10:42, Hooiveld, Guido wrote: >> -----Original Message----- >> From: Nicoline Yvonne Vanloenen [mailto:vanloen2 at lincoln.ac.nz] >> Sent: 08 August 2007 22:44 >> To: Hooiveld, Guido >> Subject: Re: [BioC] Time series analysis using predefined >> sets of genes >> >> Would you mind putting all the replies on the list? >> >> Working with time-series I would be very interested in them >> and not all of them seem to end up on the list. >> Nicoline > > Sure, though the most informative ones were from you and Ana. :-) > > Guido > > > >> --------------------------------------------------------------------- >> ----------- >> From: Nicoline Yvonne Vanloenen [mailto:vanloen2 at lincoln.ac.nz] >> Sent: 07 August 2007 23:43 >> To: Hooiveld, Guido >> Subject: Re: [BioC] Time series analysis using predefined sets of >> genes >> >> >> I use STEM to define profiles of genesets and then look for >> pathways in the different profiles, but you could try these papers >> >> >> Bar-Joseph, Z. (2004). Analyzing time series gene expression data. >> Bioinformatics (Oxford, England), 20(16), 2493-2503. >> >> >> Maraziotis, I. A., Dragomir, A., & Bezerianos, A. (2007). Gene >> networks reconstruction and time-series prediction from microarray >> data using recurrent neural fuzzy networks. IET systems biology, 1 >> (1), 41-50. > > >> -----Original Message----- >> From: Ana Conesa [mailto:aconesa at ochoa.fib.es] >> Sent: 07 August 2007 23:50 >> To: Hooiveld, Guido >> Subject: RE: [BioC] Time series analysis using predefined >> sets of genes >> >> Dear Guido >> >> Take a look to the maSigPro package and publication (Bioinformatics >> 2006 22(9):1096-1102). >> >> Ana >> > >> -----Original Message----- >> From: Daofeng Li [mailto:lidaof at gmail.com] >> Sent: 08 August 2007 03:49 >> To: Hooiveld, Guido >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Time series analysis using predefined >> sets of genes >> >> Hi, >> >> STEM is good, i am using it:) >> > > >> -----Original Message----- >> From: Nicoline Yvonne Vanloenen [mailto:vanloen2 at lincoln.ac.nz] >> Sent: 08 August 2007 22:44 >> To: Hooiveld, Guido >> Subject: Re: [BioC] Time series analysis using predefined >> sets of genes >> >> Would you mind putting all the replies on the list? >> >> Working with time-series I would be very interested in them >> and not all of them seem to end up on the list. >> Nicoline >> On 8 Aug 2007 at 20:49, Hooiveld, Guido wrote: >> >>> Thanks all for your feed-back; I certainly got some >> suggestions to go after. >>> >>> Guido >>> >>> >>> >>> ------------------------------------------------ >>> Guido Hooiveld, PhD >>> Nutrition, Metabolism & Genomics Group Division of Human Nutrition >>> Wageningen University Biotechnion, Bomenweg 2 >>> NL-6703 HD Wageningen >>> the Netherlands >>> >>> tel: (+)31 317 485788 >>> fax: (+)31 317 483342 >>> >>> internet: http://nutrigene.4t.com >>> email: guido.hooiveld at wur.nl >>> >>> >>>> -----Original Message----- >>>> From: Ana Conesa [mailto:aconesa at ochoa.fib.es] >>>> Sent: 08 August 2007 12:55 >>>> To: Hooiveld, Guido; bioconductor at stat.math.ethz.ch >>>> Cc: aconesa at cipf.es >>>> Subject: RE: [BioC] Time series analysis using predefined sets of >>>> genes >>>> >>>> Hi Guido, >>>> >>>> I am not sure if you got my early reply. >>>> You can have a look to the maSigPro package (Bioinformatics >>>> 2006 22(9):1096-1102). This will give you the gene expression >>>> pattern along time and tell you is there are significant >> changes. If >>>> you want to look for specific sets of genes you can use these as >>>> input data. >>>> I have recently developed a number of scripts (modifications of >>>> maSigPro functions) to assess significant changes for genes that >>>> share a common annotation. This I think resembles your >> question. You >>>> only need to indicate the grouping of your genes (or >>>> annotations),load the modified versions and run the program. I am >>>> enclosing you the modified functions in case you are interested. >>>> There is aslo a maSigProfunScript.R includes which tells >> a bit how >>>> to proceed. I might include this functions in a next maSigPro >>>> version... >>>> >>>> Hope this helps >>>> >>>> Ana >>>> >>>> ------------------------------------- >>>> Ana Conesa, PhD >>>> Bioinformatics Department >>>> Centro de Investigaci?n Pr?ncipe Felipe Valencia, Spain >>>> http://bioinfo.cipf.es ===================================== >>>> CAMDA2007 Conference @ CIPF >>>> http://camda.bioinfo.cipf.es >>>> ===================================== >>>> > > _______________________________________________ > 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 >