My answer is almost identical to Jims, but I wanted to mention that there are also some handy helper functions for the GO mappings such as Term() and GOID(): library(org.Hs.eg.db) library(GO.db) # here is where I thought that the helper functions might make what we are doing bit easier to see? (YMMV) goID <- GOID( GOTERM[ Term(GOTERM) == "myelination" ] ) # the rest is going to be basically the same. get(goID, org.Hs.egGO2ALLEGS) Marc On 05/18/2011 10:40 AM, James W. MacDonald wrote: > Hi Herve, > > On 5/18/2011 9:16 AM, LEMAITRE Herv? Universit? Paris Sud wrote: >> Dear bioconductor-users, >> >> >> >> I'm looking for a way to query the gene ontology in R like in the GO >> browser (AmiGO). I tried different packages (NCBI2R, GOsim ...) but I >> did not find a simple way to extract genes names associated to a GO >> term (i.e. myelination). Could you tell me if there is a way to do >> that? > > > library(org.Hs.eg.db) > > library(GO.db) > > ind <- x[x$Term == "myelination",1] > > ind > [1] "GO:0042552" > > egs <- get(ind, org.Hs.egGO2ALLEGS) > > egs > ISS ISS IEA IEA IEA IEA IEA ISS > IEA NAS > "745" "928" "1000" "1959" "2064" "3073" "3074" "3170" > "3611" "4118" > TAS IEA IEA IEA ISS IEA IEA IEA > IEA IEA > "4118" "4155" "4664" "4665" "4763" "4908" "5354" "5376" > "5453" "5454" > NAS ISS ISS IEA ISS IEA IEA IEA > ISS IEA > "5653" "6326" "6334" "6497" "6647" "7038" "7040" "7248" > "7572" "8443" > IMP IMP IMP ISS IEA ISS IEA IEA > ISS ISS > "8890" "8892" "8893" "9451" "9514" "9921" "10215" "10939" > "11202" "23114" > NAS ISS IEA IEA ISS NAS IEA > "23205" "23405" "50846" "51090" "57463" "81846" "84504" > > You could filter at this point, if you wanted e.g., just ISS terms. > > > genes <- unlist(mget(egs, org.Hs.egSYMBOL)) > > genes > 745 928 1000 1959 2064 3073 3074 > 3170 > "C11orf9" "CD9" "CDH2" "EGR2" "ERBB2" "HEXA" "HEXB" > "FOXA2" > 3611 4118 4118 4155 4664 4665 4763 > 4908 > "ILK" "MAL" "MAL" "MBP" "NAB1" "NAB2" "NF1" > "NTF3" > 5354 5376 5453 5454 5653 6326 6334 > 6497 > "PLP1" "PMP22" "POU3F1" "POU3F2" "KLK6" "SCN2A" "SCN8A" > "SKI" > 6647 7038 7040 7248 7572 8443 8890 > 8892 > "SOD1" "TG" "TGFB1" "TSC1" "ZNF24" "GNPAT" "EIF2B4" > "EIF2B2" > 8893 9451 9514 9921 10215 10939 11202 > 23114 > "EIF2B5" "EIF2AK3" "GAL3ST1" "RNF10" "OLIG2" "AFG3L2" "KLK8" > "NFASC" > 23205 23405 50846 51090 57463 81846 84504 > "ACSBG1" "DICER1" "DHH" "PLLP" "AMIGO1" "SBF2" "NKX6-2" > > Best, > > Jim > > >> >> >> >> Thanks, >> >> >> >> Herv? >> >> >> >> >> >> `?.??.????``?.??.????``?.??.????``?.??.????``?.??.????``?.??.????`` ?.??.????``?.??.????``?.??.????``?.??.?? >> >> >> Herv? Lema?tre >> >> U1000 "Imagerie et Psychiatrie" >> >> INSERM - CEA - Facult? de M?decine Paris Sud 11 >> >> Service Hospitalier Fr?d?ric Joliot >> >> 4, Place du G?n?ral Leclerc >> >> 91401 ORSAY, FRANCE >> >> T?l: (+33) 1 69 86 77 84 >> >> Fax: (+33) 1 69 86 78 10 >> >> `?.??.????``?.??.????``?.??.????``?.??.????``?.??.????``?.??.????`` ?.??.????``?.??.????``?.??.????``?.??.?? >> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> >> _______________________________________________ Bioconductor mailing >> list Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >> archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >