{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T11:08:05Z","timestamp":1788347285374,"version":"build-2803163510"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The R\/Bioconductor package RamiGO is an R interface to AmiGO that enables visualization of Gene Ontology (GO) trees. Given a list of GO terms, RamiGO uses the AmiGO visualize API to import Graphviz-DOT format files into R, and export these either as images (SVG, PNG) or into Cytoscape for extended network analyses. RamiGO provides easy customization of annotation, highlighting of specific GO terms, colouring of terms by P-value or export of a simplified summary GO tree. We illustrate RamiGO functionalities in a genome-wide gene set analysis of prognostic genes in breast cancer.<\/jats:p>\n               <jats:p>Availability and implementation: RamiGO is provided in R\/Bioconductor, is open source under the Artistic-2.0 License and is available with a user manual containing installation, operating instructions and tutorials. It requires R version 2.15.0 or higher. URL: http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/RamiGO.html<\/jats:p>\n               <jats:p>Contact: \u00a0markus.schroeder@ucdconnect.ie<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts708","type":"journal-article","created":{"date-parts":[[2013,1,8]],"date-time":"2013-01-08T23:12:01Z","timestamp":1357686721000},"page":"666-668","source":"Crossref","is-referenced-by-count":23,"title":["RamiGO: an R\/Bioconductor package providing an AmiGO Visualize interface"],"prefix":"10.1093","volume":"29","author":[{"given":"Markus S.","family":"Schr\u00f6der","sequence":"first","affiliation":[{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"},{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Gusenleitner","sequence":"additional","affiliation":[{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"},{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Quackenbush","sequence":"additional","affiliation":[{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"},{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"},{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aed\u00edn C.","family":"Culhane","sequence":"additional","affiliation":[{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"},{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Haibe-Kains","sequence":"additional","affiliation":[{"name":"1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, 2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 3Department of Bioinformatics, Boston University, Boston, MA 02215, USA, 4Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, 5Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA and 6Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montr\u00e9al, Montreal, Quebec H2W 1R7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,1,6]]},"reference":[{"key":"2023051607330718600_bts708-B1","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/bioinformatics\/btn615","article-title":"AmiGO: online access to ontology and annotation data","volume":"25","author":"Carbon","year":"2009","journal-title":"Bioinformatics"},{"key":"2023051607330718600_bts708-B2","article-title":"The Gene Ontology: enhancements for 2011","author":"Gene Ontology Consortium","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023051607330718600_bts708-B3","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1002\/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N","article-title":"An open graph visualization system and its applications to software engineering","volume":"30","author":"Gansner","year":"2000","journal-title":"Software Practice and Experience"},{"key":"2023051607330718600_bts708-B4","doi-asserted-by":"crossref","first-page":"6740","DOI":"10.1073\/pnas.0701138104","article-title":"Lung metastasis genes couple breast tumor size and metastatic spread","volume":"104","author":"Minn","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023051607330718600_bts708-B5","doi-asserted-by":"crossref","first-page":"3206","DOI":"10.1093\/bioinformatics\/btr511","article-title":"survcomp: an R\/Bioconductor package for performance assessment and comparison of survival models","volume":"27","author":"Schr\u00f6der","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051607330718600_bts708-B6","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023051607330718600_bts708-B7","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/S0140-6736(05)17947-1","article-title":"Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer","volume":"365","author":"Wang","year":"2005","journal-title":"Lancet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/5\/666\/50335754\/bioinformatics_29_5_666.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/5\/666\/50335754\/bioinformatics_29_5_666.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T07:55:47Z","timestamp":1684223747000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/5\/666\/247703"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,6]]},"references-count":7,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2013,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts708","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,3,1]]},"published":{"date-parts":[[2013,1,6]]}}}