{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T03:28:57Z","timestamp":1778642937951,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Connections between disease phenotypes and drug effects can be made by identifying commonalities in the associated patterns of differential gene expression. Searchable databases that record the impacts of chemical or genetic perturbations on the transcriptome\u2014here referred to as \u2018connectivity maps\u2019\u2014permit discovery of such commonalities. We describe two R packages, gCMAP and gCMAPWeb, which provide a complete framework to construct and query connectivity maps assembled from user-defined collections of differential gene expression data. Microarray or RNAseq data are processed in a standardized way, and results can be interrogated using various well-established gene set enrichment methods. The packages also feature an easy-to-deploy web application that facilitates reproducible research through automatic generation of graphical and tabular reports.<\/jats:p>\n               <jats:p>Availability and implementation: The gCMAP and gCMAPWeb R packages are freely available for UNIX, Windows and Mac OS X operating systems at Bioconductor (http:\/\/www.bioconductor.org).<\/jats:p>\n               <jats:p>Contact: \u00a0bourgon.richard@gene.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt592","type":"journal-article","created":{"date-parts":[[2013,10,17]],"date-time":"2013-10-17T01:33:55Z","timestamp":1381973635000},"page":"127-128","source":"Crossref","is-referenced-by-count":17,"title":["gCMAP: user-friendly connectivity mapping with R"],"prefix":"10.1093","volume":"30","author":[{"given":"Thomas","family":"Sandmann","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah K.","family":"Kummerfeld","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Gentleman","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Bourgon","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,10,15]]},"reference":[{"key":"2023012710371550600_btt592-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023012710371550600_btt592-B2","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1093\/bioinformatics\/btr296","article-title":"Model-based gene set analysis for bioconductor","volume":"27","author":"Bauer","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012710371550600_btt592-B3","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/onc.2011.228","article-title":"Modulation of wnt\/-catenin signaling and proliferation by a ferrous iron chelator with therapeutic efficacy in genetically engineered mouse models of cancer","volume":"31","author":"Coombs","year":"2012","journal-title":"Oncogene"},{"key":"2023012710371550600_btt592-B4","doi-asserted-by":"crossref","first-page":"96ra76","DOI":"10.1126\/scitranslmed.3002648","article-title":"Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease","volume":"3","author":"Dudley","year":"2011","journal-title":"Sci Transl Med"},{"key":"2023012710371550600_btt592-B5","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1093\/bioinformatics\/btl599","article-title":"Extensions to gene set enrichment","volume":"23","author":"Jiang","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012710371550600_btt592-B6","doi-asserted-by":"crossref","DOI":"10.1111\/j.1538-7836.2012.04930.x","article-title":"Reactome\u2014a curated knowledgebase of biological pathways: megakaryocytes and platelets","author":"Jupe","year":"2012","journal-title":"J. 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