[BioC] Time series analysis using predefined sets of genes

[Martino Barenco]

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=f100 
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 Investigación Príncipe Felipe Valencia, Spain
>>>> http://bioinfo.cipf.es =====================================
>>>> CAMDA2007 Conference @ CIPF
>>>> http://camda.bioinfo.cipf.es
>>>> =====================================
>>>>
>
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