[BioC] hyperG over chromosome position...?

[Dario Greco]

hi all,
thanks a lot for your emails and for implementing something (too  
late, you kind of promised now)! :)
i will not even try, as i am far away from being a proper developer,  
i guess :)

I agree that in many cases the chromosomal location is not  
biologically relevant, but there are some situations where it might  
be interesting to investigate.

i am right now working with two different datasets:
1) a dataset where the subject is Down Syndrome. of course it could  
sound stupid, but still nice to provide statistics for the massive  
chr21 upregulation :)
moreover, there are interesting issues of "critical regions" for  
diseases that are associated to DS and that have been historically  
described in certain cytobands of chr21 (eg. AtrioVentricular Septal  
Defect - AVSD - having probably 21q2.3 as critical region) .
2) a dataset where the subject is Tybe 2 Diabetes where i apparently  
observe clusters of dis-regulated genes located into the same  
chromosomal regions.

besides these autobiographic stories, there are appealing theories  
inferring  that co-regulated genes might sit (sometimes) close to  
each other onto the same chromosomal region, to my understanding.

i anyway agree with the fact that cytobands don't represent a very  
meaningful way to define chromatin "spots", but they are quite easy  
to deal with. definitely it would be much better to have something  
more "biological" to split the chromosomes!

thanks again for your attention and help!
sincerely
d

-- 

Dario Greco

Institute of Biotechnology - University of Helsinki
Building Cultivator II
P.O.Box 56    Viikinkaari 4
FIN-00014    Finland

Office: +358 9 191 58951
Fax: +358 9 191 58952
Mobile: +358 44 023 5780

Lab WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/

Personal WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm

-- 

Dario Greco

Institute of Biotechnology - University of Helsinki
Building Cultivator II
P.O.Box 56    Viikinkaari 4
FIN-00014    Finland

Office: +358 9 191 58951
Fax: +358 9 191 58952
Mobile: +358 44 023 5780

Lab WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/

Personal WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm



On Jan 16, 2007, at 8:29 PM, Robert Gentleman wrote:

> Hi,
>   Just a couple of notes,
> 1) chromosomal location is typically not biologically relevant in  
> higher organisms, AFAIK. Since I work at a cancer center, and since  
> some (but by no means all) genomic abnormalities in cancer induce  
> an effect that can be detected by chromosomal location these sorts  
> of things are interesting to me. Anyone using this approach should,  
> IMHO, have a sound biological reason for doing so.
>
> 2) Chromosome bands are probably not ideal (as Francois so  
> correctly points out), but they have the advantage of being easily  
> obtained. Other options will require more effort.
>
> 3) the code that does this in the Category package and is called  
> MAPAmat, but it is flawed in a number of ways. Seth and I will put  
> something up that is better in a week or two.
>
> 4) any other contributions are welcome, particularly well  
> implemented and documented functions.
>
>  best wishes
>    Robert
>
> Francois Pepin wrote:
>> Hi Dario,
>> It is possible to do it with the chromosomal band using Category.  
>> That
>> was the last part of Robert Gentleman's Category tutorial at BioC2006
>> (http://www.bioconductor.org/workshops/2006/BioC2006/labs/ 
>> rgentleman/).
>> I'm not convinced if the chromosomal bands are the best partition  
>> to use
>> in that case, but it's a good starting point.
>> Francois
>> On Tue, 2007-01-16 at 07:43 -0800, Seth Falcon wrote:
>>> Hi Dario,
>>>
>>>>> Dario Greco wrote:
>>>>>> hi all,
>>>>>> i would like to perform hyperGTest using the chromosome  
>>>>>> position   (stored usually in pkgMAP environment).
>>>>>> how could it be possible?
>>> Actually, this is on my list of things to add to the Category
>>> package.  If you, or anyone, wants to do some programming, take a  
>>> look
>>> at how the KEGG and PFAM tests are implemented.  A first pass for
>>> chromosome position will be quite similar.
>>>
>>> + seth
>>>
>>> --
>>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer  
>>> Research Center
>>> http://bioconductor.org
>>>
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>
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org