[BioC] Time series analysis using predefined sets of genes

[Hooiveld, Guido]

> -----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 Investigación Príncipe Felipe Valencia, Spain 
> > > http://bioinfo.cipf.es =====================================
> > > CAMDA2007 Conference @ CIPF
> > > http://camda.bioinfo.cipf.es
> > > =====================================
> > >