{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T08:11:55Z","timestamp":1778659915903,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,15]]},"abstract":"<jats:title>Summary<\/jats:title>\n               <jats:p>Alternate promoter usage is an important molecular mechanism for generating RNA and protein diversity. Cap Analysis Gene Expression (CAGE) is a powerful approach for revealing the multiplicity of transcription start site (TSS) events across experiments and conditions. An understanding of the dynamics of TSS choice across these conditions requires both sensitive quantification and comparative visualization. We have developed CAGExploreR, an R package to detect and visualize changes in the use of specific TSS in wider promoter regions in the context of changes in overall gene expression when comparing different CAGE samples. These changes provide insight into the modification of transcript isoform generation and regulatory network alterations associated with cell types and conditions. CAGExploreR is based on the FANTOM5 and MPromDb promoter set definitions but can also work with user-supplied regions. The package compares multiple CAGE libraries simultaneously. Supplementary Materials describe methods in detail, and a vignette demonstrates a workflow with a real data example.<\/jats:p>\n               <jats:p>Availability and implementation: The package is freely available under the MIT license from CRAN (http:\/\/cran.r-project.org\/web\/packages\/CAGExploreR).<\/jats:p>\n               <jats:p>Contact: \u00a0edimont@mail.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu125","type":"journal-article","created":{"date-parts":[[2014,3,28]],"date-time":"2014-03-28T03:43:36Z","timestamp":1395978216000},"page":"1183-1184","source":"Crossref","is-referenced-by-count":5,"title":["CAGExploreR: an R package for the analysis and visualization of\n                    promoter dynamics across multiple experiments"],"prefix":"10.1093","volume":"30","author":[{"given":"Emmanuel","family":"Dimont","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oliver","family":"Hofmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shannan J","family":"Ho Sui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alistair R R","family":"Forrest","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hideya","family":"Kawaji","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Winston","family":"Hide","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"the FANTOM Consortium","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,3,26]]},"reference":[{"key":"2023012710491012300_btu125-B1","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/ng1789","article-title":"Genome-wide analysis of mammalian promoter architecture and evolution","volume":"38","author":"Carninci","year":"2006","journal-title":"Nat. Genet."},{"key":"2023012710491012300_btu125-B2","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"ENCODE Consortium","year":"2012","journal-title":"Nature"},{"key":"2023012710491012300_btu125-B3","article-title":"A promoter level mammalian expression atlas","author":"Forrest","year":"2014","journal-title":"Nature"},{"key":"2023012710491012300_btu125-B4","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkq1171","article-title":"MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data","volume":"39","author":"Gupta","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012710491012300_btu125-B5","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1101\/gr.120535.111","article-title":"Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development","volume":"21","author":"Pal","year":"2011","journal-title":"Genome Res."},{"key":"2023012710491012300_btu125-B6","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1038\/nmeth.1470","article-title":"Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan","volume":"7","author":"Plessy","year":"2010","journal-title":"Nat. Methods"},{"key":"2023012710491012300_btu125-B7","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012710491012300_btu125-B8","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1086\/224909","article-title":"On the estimation of relationships involving qualitative variables","volume":"76","author":"Theil","year":"1970","journal-title":"Am. J. Sociol."},{"key":"2023012710491012300_btu125-B9","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1186\/1471-2164-12-505","article-title":"Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis","volume":"12","author":"Thorsen","year":"2011","journal-title":"BMC Genomics"},{"key":"2023012710491012300_btu125-B10","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/8\/1183\/48922823\/bioinformatics_30_8_1183.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/8\/1183\/48922823\/bioinformatics_30_8_1183.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:25:59Z","timestamp":1674818759000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/8\/1183\/2748133"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,3,26]]},"references-count":10,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2014,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu125","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2014,4,15]]},"published":{"date-parts":[[2014,3,26]]}}}