Hi Ricardo, I have not thought of that. it's simple. Thank you very much ! Jean-Pierre Ricardo a ?crit : > Hi Jean-Pierre, > > I assume you were using TopGO from the message header, > so you can do the following: > > # sample are your candidate genes and allgenes all other genes > # you included in your analysis > > universe = factor(as.integer(allgenes %in% sample)) > names(universe) = allgenes > > # you created an GOdata object for TopGO > # "GO" would be your annotation Gene2GOid list > > GOdata = new('topGOdata',ontology="BP",allGenes=universe, > annot=annFUN.gene2GO,gene2GO=GO) > > # retrieve genes2GO list from the "expanded" annotation in GOdata > > allGO = genesInTerm(GOdata) > > #allGO["GO:0000109"] > #$`GO:0000109` > #[1] "ENSG00000012061" "ENSG00000104472" "ENSG00000175595" > > SAM_ANOTATION = lapply(allGO,function(x) x[x %in% sample] ) > > # Your significant genes for GO:0051427 > SAM_ANOTATION[["GO:0051427"]] > > Hope it was helpful. > Best wishes, > Ricardo > > > Jean-Pierre Desvignes wrote: >> Hello, >> >> I would known if it was possible to retrieve the genes related to a >> GO term ? >> >> If yes, how to do that ? >> >> GO.ID Term Level Annotated "Significant" Expected classicFisher >> >> GO:0051427 hormone receptor binding 5 16 17 "2" 0.12 0.00583 >> >> For example, what are the 2 Significant genes here ? >> >> >> >> Thanks a lot. >> >> _______________________________________________ >> 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 >> >> > > -- Jean-Pierre Desvignes Ing?nieur d'?tude. Plateforme Montpellier GenomiX Institut de G?nomique Fonctionnelle 141 rue de la Cardonille 34094 Montpellier cedex 05 -FRANCE- T?l: 04.67.14.29.32 -- Passerelle antivirus IGF --