Hi Bernardo, this is normal and it is a consequence of the True Path Rule. After all, you want to perform the enrichment test on the GO ontology not only on a selected number of GO terms. Regards, Adrian On Tue, Oct 29, 2013 at 7:20 PM, Bernardo Bello <popnard@gmail.com> wrote: > Possible answer -> These new GO terms seem to be the parents of the already > GO terms present in my original dataset. > > Original question: > > Hi there, > > I ran an enrichment analysis with custom annotations using TopGO and > surprisingly I obtained new GO terms inside the significant GO terms. > > Is that possible? The only reason I can imagine this is possible is > because TopGO adds new GO terms based on the input GO terms, since GO > ontology is structured hierarchically. > > Please let me know if you need more details about the experiment. > > Code: > > > https://drive.google.com/file/d/0B8-ZAuZe8jldbjNuTHhNeXRVX00/edit?us p=sharing > > TopGO output: > > > https://drive.google.com/file/d/0B8-ZAuZe8jldZnlYUzlxZ3psMWc/edit?us p=sharing > > Thanks, Bernardo > > > -- > > *Bernardo Bello Ortí* > > PhD student > > CReSA-IRTA > > Campus de Bellaterra-Universitat Autònoma de Barcelona > > Edifici CReSA > > 08193 Bellaterra (Barcelona, Spain) > > Tel.: 647 42 52 63 *www.cresa.es * > > * > * > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Thanks for the clarification Adrian. Could you please recommend some key publications about GO terminology? I would like to understand this more in depth. Bernardo 2013/11/1 Adrian Alexa <adrian.alexa@gmail.com> > Hi Bernardo, > > this is normal and it is a consequence of the True Path Rule. After all, > you want to perform the enrichment test on the GO ontology not only on a > selected number of GO terms. > > Regards, > Adrian > > > > > On Tue, Oct 29, 2013 at 7:20 PM, Bernardo Bello <popnard@gmail.com> wrote: > >> Possible answer -> These new GO terms seem to be the parents of the >> already >> GO terms present in my original dataset. >> >> Original question: >> >> Hi there, >> >> I ran an enrichment analysis with custom annotations using TopGO and >> surprisingly I obtained new GO terms inside the significant GO terms. >> >> Is that possible? The only reason I can imagine this is possible is >> because TopGO adds new GO terms based on the input GO terms, since GO >> ontology is structured hierarchically. >> >> Please let me know if you need more details about the experiment. >> >> Code: >> >> >> https://drive.google.com/file/d/0B8-ZAuZe8jldbjNuTHhNeXRVX00/edit?u sp=sharing >> >> TopGO output: >> >> >> https://drive.google.com/file/d/0B8-ZAuZe8jldZnlYUzlxZ3psMWc/edit?u sp=sharing >> >> Thanks, Bernardo >> >> >> -- >> >> *Bernardo Bello Ortí* >> >> >> PhD student >> >> CReSA-IRTA >> >> Campus de Bellaterra-Universitat Autònoma de Barcelona >> >> Edifici CReSA >> >> 08193 Bellaterra (Barcelona, Spain) >> >> Tel.: 647 42 52 63 *www.cresa.es * >> >> * >> * >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es * * * [[alternative HTML version deleted]]