{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:36:16Z","timestamp":1761489376740},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,1]]},"abstract":"<jats:p>Motivation: RNA-seq techniques generate massive amounts of expression data. Several pipelines (e.g. Tophat and Cufflinks) are broadly applied to analyse these datasets. However, accessing and handling the analytical output remain challenging for non-experts.<\/jats:p>\n               <jats:p>Results: We present the RNASeqExpressionBrowser, an open-source web interface that can be used to access the output from RNA-seq expression analysis packages in different ways, as it allows browsing for genes by identifiers, annotations or sequence similarity. Gene expression information can be loaded as long as it is represented in a matrix-like format. Additionally, data can be made available by setting up the tool on a public server. For demonstration purposes, we have set up a version providing expression information from the barley genome.<\/jats:p>\n               <jats:p>Availability and implementation: The source code and a show case are accessible at http:\/\/mips.helmholtz-muenchen.de\/plant\/RNASeqExpressionBrowser\/.<\/jats:p>\n               <jats:p>Contact: \u00a0k.mayer@helmholtz-muenchen.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu334","type":"journal-article","created":{"date-parts":[[2014,5,16]],"date-time":"2014-05-16T01:21:59Z","timestamp":1400203319000},"page":"2519-2520","source":"Crossref","is-referenced-by-count":21,"title":["RNASeqExpressionBrowser\u2014a web interface to browse and visualize high-throughput expression data"],"prefix":"10.1093","volume":"30","author":[{"given":"Thomas","family":"Nussbaumer","sequence":"first","affiliation":[{"name":"1Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Center Munich, National Research Center for Environment and Health, 85764 Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karl G.","family":"Kugler","sequence":"additional","affiliation":[{"name":"1Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Center Munich, National Research Center for Environment and Health, 85764 Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai C.","family":"Bader","sequence":"additional","affiliation":[{"name":"1Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Center Munich, National Research Center for Environment and Health, 85764 Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sapna","family":"Sharma","sequence":"additional","affiliation":[{"name":"1Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Center Munich, National Research Center for Environment and Health, 85764 Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Seidel","sequence":"additional","affiliation":[{"name":"1Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Center Munich, National Research Center for Environment and Health, 85764 Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Klaus F. X.","family":"Mayer","sequence":"additional","affiliation":[{"name":"1Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Center Munich, National Research Center for Environment and Health, 85764 Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,5,14]]},"reference":[{"key":"2023012711525461900_btu334-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped blast and psi-blast: a new generation of protein database search programs","volume":"17","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012711525461900_btu334-B2","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":"2023012711525461900_btu334-B3","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/nature11650","article-title":"Analysis of the bread wheat genome using whole-genome shotgun sequencing","volume":"491","author":"Brenchley","year":"2012","journal-title":"Nature"},{"key":"2023012711525461900_btu334-B4","doi-asserted-by":"crossref","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The gene ontology (go) database and informatics resource","volume":"32","author":"Gene Ontology Consortium","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012711525461900_btu334-B6","doi-asserted-by":"crossref","first-page":"W622","DOI":"10.1093\/nar\/gks540","article-title":"RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics","volume":"40","author":"Lohse","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012711525461900_btu334-B7","doi-asserted-by":"crossref","first-page":"D1144","DOI":"10.1093\/nar\/gks1153","article-title":"MIPS PlantsDB: a database framework for comparative plant genome research","volume":"41","author":"Nussbaumer","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012711525461900_btu334-B8","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":"2023012711525461900_btu334-B9","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/nature11543","article-title":"A physical, genetic and functional sequence assembly of the barley genome","volume":"491","author":"The International Barley Sequencing Consortium","year":"2012","journal-title":"Nature"},{"key":"2023012711525461900_btu334-B10","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711525461900_btu334-B5","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat Protoc"},{"key":"2023012711525461900_btu334-B11","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with rna-seq","volume":"28","author":"Trapnell","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"2023012711525461900_btu334-B12","doi-asserted-by":"crossref","first-page":"3204","DOI":"10.1093\/bioinformatics\/btt558","article-title":"STAR: an integrated solution to management and visualization of sequencing data","volume":"29","author":"Wang","year":"2013","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2519\/48927340\/bioinformatics_30_17_2519.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2519\/48927340\/bioinformatics_30_17_2519.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:15:58Z","timestamp":1674821758000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/17\/2519\/2748233"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,14]]},"references-count":12,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2014,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu334","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,14]]}}}