Hello, Is it possible to recover a full list of genes associated with a significantly enriched GO term? I am using custom annotation in the GO2gene format. Best wishes, Agnieszka -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] topGO_2.12.0 SparseM_1.03 GO.db_2.9.0 [4] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 [7] Biobase_2.20.1 BiocGenerics_0.6.0 graph_1.38.3 loaded via a namespace (and not attached): [1] grid_3.0.1 IRanges_1.18.4 lattice_0.20-27 stats4_3.0.1 [5] tools_3.0.1 -- Sent via the guest posting facility at bioconductor.org.

Agnieszka it depends on the species and gene identifier system that you are looking for. Assuming that you want to get Ensembl Gene-IDs in Homo Sapiens, then something like the below will do. library('org.Hs.eg.db') key = 'GO:0043586' columns = c('ENSEMBL', 'GENENAME') s = select(org.Hs.eg.db, key, columns, keytype='GO') print(s) There are also alternative facilities in the biomaRt package. Wolfgang Il giorno 07 Jun 2014, alle ore 00:55, Agnieszka Golicz [guest] <guest at="" bioconductor.org=""> ha scritto: > Hello, > > Is it possible to recover a full list of genes associated with a significantly enriched GO term? > > I am using custom annotation in the GO2gene format. > > > Best wishes, > Agnieszka > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] topGO_2.12.0 SparseM_1.03 GO.db_2.9.0 > [4] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 > [7] Biobase_2.20.1 BiocGenerics_0.6.0 graph_1.38.3 > > loaded via a namespace (and not attached): > [1] grid_3.0.1 IRanges_1.18.4 lattice_0.20-27 stats4_3.0.1 > [5] tools_3.0.1 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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