Sure. Maybe it's something that is clear to a biologist and I (as a physicist) cannot read in-between the lines. I redirected my question to a biologist at the Temple University whom we collaborate with. ... In fact I proposed to leave those miRNAs out of the validation table we are building. He disapproved. If he does not come up with the sequence then I will try to contact the paper authors. Maura -----Messaggio originale----- Da: seandavi@gmail.com per conto di Sean Davis Inviato: mar 18/05/2010 17.21 A: mauede@alice.it Cc: Heidi Dvinge; Bioconductor List Oggetto: Re: [BioC] R: Redirection of Silencing Targets by Adenosine- to-Inosine Editing of miRNAs On Tue, May 18, 2010 at 11:04 AM, <mauede@alice.it> wrote: > I read the paper by Kawahara et al, 2007 in advance of posting my question. > It seems to me (I am not a biologist) that the articlle explains the > discovery and > implications of edited miRNAs ... There is also a nice picture. But I > cannot read out any > sequence. > > Hi, Maura. You could write to the author of that reference if the paper is unclear. Sean > -----Messaggio originale----- > Da: Heidi Dvinge [mailto:heidi@ebi.ac.uk] > Inviato: mar 18/05/2010 15.47 > A: mauede@alice.it > Cc: Bioconductor List > Oggetto: Re: [BioC] Redirection of Silencing Targets by > Adenosine-to-Inosine Editing of miRNAs > > Dear Maura, > > your best bet here is probably the article that the data in TarBase > was taken from. There's a reference for each entry; you can check > those manually. > > Best > \Heidi > > On 18 May 2010, at 14:38, <mauede@alice.it> <mauede@alice.it> wrote: > > > TarBase contains some miRNAs that have undergone the biological > > editing process. > > No sequence, though, is available for such "transformed" miRNAs. > > I wonder whether the sequences for such miRNAs are stored in some > > database. > > > > Thank you in advance for any suggestion. > > Maura > > > > > > tutti i telefonini TIM! > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/ > > gmane.science.biology.informatics.conductor > > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > tutti i telefonini TIM! [[alternative HTML version deleted]]

On Tue, May 18, 2010 at 11:32 AM, <mauede@alice.it> wrote: > Sure. Maybe it's something that is clear to a biologist and I (as a > physicist) cannot read in-between the lines. > I redirected my question to a biologist at the Temple University whom we > collaborate with. ... In fact I proposed to leave those > miRNAs out of the validation table we are building. He disapproved. > If he does not come up with the sequence then I will try to contact the > paper authors. > > This is the correct model, in my mind. Collaboration with a biologist is often the most productive way of working and is usually preferred over an email list (at least by me--others may disagree here). Many of the folks on this list are not biologists either, so you are not unusual from this point of view. Sean > -----Messaggio originale----- > Da: seandavi@gmail.com per conto di Sean Davis > Inviato: mar 18/05/2010 17.21 > A: mauede@alice.it > Cc: Heidi Dvinge; Bioconductor List > Oggetto: Re: [BioC] R: Redirection of Silencing Targets by > Adenosine-to-Inosine Editing of miRNAs > > On Tue, May 18, 2010 at 11:04 AM, <mauede@alice.it> wrote: > > > I read the paper by Kawahara et al, 2007 in advance of posting my > question. > > It seems to me (I am not a biologist) that the articlle explains the > > discovery and > > implications of edited miRNAs ... There is also a nice picture. But I > > cannot read out any > > sequence. > > > > > Hi, Maura. You could write to the author of that reference if the paper is > unclear. > > Sean > > > > > -----Messaggio originale----- > > Da: Heidi Dvinge [mailto:heidi@ebi.ac.uk] > > Inviato: mar 18/05/2010 15.47 > > A: mauede@alice.it > > Cc: Bioconductor List > > Oggetto: Re: [BioC] Redirection of Silencing Targets by > > Adenosine-to-Inosine Editing of miRNAs > > > > Dear Maura, > > > > your best bet here is probably the article that the data in TarBase > > was taken from. There's a reference for each entry; you can check > > those manually. > > > > Best > > \Heidi > > > > On 18 May 2010, at 14:38, <mauede@alice.it> <mauede@alice.it> wrote: > > > > > TarBase contains some miRNAs that have undergone the biological > > > editing process. > > > No sequence, though, is available for such "transformed" miRNAs. > > > I wonder whether the sequences for such miRNAs are stored in some > > > database. > > > > > > Thank you in advance for any suggestion. > > > Maura > > > > > > > > > tutti i telefonini TIM! > > > > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: http://news.gmane.org/ > > > gmane.science.biology.informatics.conductor > > > > > > > > > > > > tutti i telefonini TIM! > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]