Dario Greco wrote: > 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 :) umm, if you look at the figure on p 179 of our monograph, you will see that there is no such massive up-regulation (at least for the data presented there). A blunt instrument is unlikely to detect the sorts of changes (at least on a single sample basis) that might be of interest. > 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. yes, and hopefully the facts will coincide - as I said there are certainly some biological reasons for this sort of behavior, in some diseases. Fishing expeditions are IMHO unlikely to be useful. > > 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/rgentlem an/). >>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> _______________________________________________ >>> 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 >> >> --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 > > -- 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