{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T03:49:31Z","timestamp":1789962571801,"version":"4.0.1"},"reference-count":36,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2018,5,16]],"date-time":"2018-05-16T00:00:00Z","timestamp":1526428800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["MetastaSys (0316173A)"],"award-info":[{"award-number":["MetastaSys (0316173A)"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bundesministerium f\u00fcr Bildung und Forschung (DE)","award":["MyPathSem (031L0024)"],"award-info":[{"award-number":["MyPathSem (031L0024)"]}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["HER2LOW (031A429)"],"award-info":[{"award-number":["HER2LOW (031A429)"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["MMML-Demonstrators (031A428)"],"award-info":[{"award-number":["MMML-Demonstrators (031A428)"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["Open Access Publication Funds of the G\u00f6ttingen University"],"award-info":[{"award-number":["Open Access Publication Funds of the G\u00f6ttingen University"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0197162","type":"journal-article","created":{"date-parts":[[2018,5,16]],"date-time":"2018-05-16T17:44:06Z","timestamp":1526492646000},"page":"e0197162","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells"],"prefix":"10.1371","volume":"13","author":[{"given":"Alexander","family":"Wolff","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michaela","family":"Bayerlov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jochen","family":"Gaedcke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dieter","family":"Kube","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6509-2143","authenticated-orcid":true,"given":"Tim","family":"Bei\u00dfbarth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,5,16]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Z Wang","year":"2009","journal-title":"Nat Rev Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nrg2934","article-title":"RNA sequencing: advances, challenges and opportunities","volume":"12","author":"F Ozsolak","year":"2011","journal-title":"Nat Rev Genet"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/nrg3722","article-title":"The rise of regulatory RNA","volume":"15","author":"KV Morris","year":"2014","journal-title":"Nat Rev Genet"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1093\/bioinformatics\/btq040","article-title":"SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors","volume":"26","author":"R Goya","year":"2010","journal-title":"Bioinformatics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"e58815","DOI":"10.1371\/journal.pone.0058815","article-title":"Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data","volume":"8","author":"EM Quinn","year":"2013","journal-title":"PLoS ONE"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e172","DOI":"10.1093\/nar\/gku1005","article-title":"The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data","volume":"42","author":"X Tang","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/nrg2626","article-title":"Sequencing technologies\u2014the next generation","volume":"11","author":"ML Metzker","year":"2010","journal-title":"Nat Rev Genet"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2010-11-12-220","article-title":"From RNA-seq reads to differential expression results","volume":"11","author":"A Oshlack","year":"2010","journal-title":"Genome Biol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"D1113","DOI":"10.1093\/nar\/gku1057","article-title":"ArrayExpress update\u2014simplifying data submissions","volume":"43","author":"N Kolesnikov","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2014update","volume":"41","author":"T Barrett","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1038\/nbt.2957","article-title":"A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium","volume":"32","author":"Z Su","year":"2014","journal-title":"Nat Biotechnol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"3707","DOI":"10.1073\/pnas.1019753108","article-title":"Human transcriptome array for high-throughput clinical studies","volume":"108","author":"W Xu","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-14-370","article-title":"Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching","volume":"14","author":"H Rehrauer","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e78644","DOI":"10.1371\/journal.pone.0078644","article-title":"Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells","volume":"9","author":"S Zhao","year":"2014","journal-title":"PLoS ONE"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1038\/nbt1239","article-title":"The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements","volume":"24","author":"L Shi","year":"2006","journal-title":"Nat Biotechnol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nbt.1665","article-title":"The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models","volume":"28","author":"L Shi","year":"2010","journal-title":"Nat Biotechnol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1002\/ijc.20759","article-title":"The Epstein-Barr virus oncoprotein latent membrane protein 1 induces expression of the chemokine IP-10: Importance of mRNA half-life regulation","volume":"114","author":"M Vockerodt","year":"2005","journal-title":"Int J Cancer"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1478-811X-10-43","article-title":"Global gene expression changes of in vitro stimulated human transformed germinal centre B cells as surrogate for oncogenic pathway activation in individual aggressive B cell lymphomas","volume":"10","author":"A Schrader","year":"2012","journal-title":"Cell Commun Signal"},{"key":"ref19","unstructured":"R Development Core Team. R: A Language and Environment for Statistical Computing. 2008; <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.R-project.org\" xlink:type=\"simple\">http:\/\/www.R-project.org<\/ext-link>"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"RA Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2202\/1544-6115.1027","article-title":"Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments","volume":"3","author":"GK Smyth","year":"2004","journal-title":"Stat Appl Genet Mol Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B Methodol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"D Kim","year":"2013","journal-title":"Genome Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1038\/nbt.2862","article-title":"Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms","volume":"32","author":"R Patro","year":"2014","journal-title":"Nat Biotechnol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"S Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"B Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref28","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":"C Trapnell","year":"2010","journal-title":"Nat Biotechnol"},{"key":"ref29","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":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref30","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":"C Trapnell","year":"2012","journal-title":"Nat Protoc"},{"key":"ref31","unstructured":"Alexa A, Rahnenfuhrer J. topGO: topGO: Enrichment analysis for Gene Ontology. 2010."},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1101\/gr.079558.108","article-title":"RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays","volume":"18","author":"JC Marioni","year":"2008","journal-title":"Genome Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1186\/1471-2164-11-282","article-title":"A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling","volume":"11","author":"JR Bradford","year":"2010","journal-title":"BMC Genomics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"e141","DOI":"10.1093\/nar\/gkn705","article-title":"Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms","volume":"36","author":"PAC \u2018t Hoen","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e71462","DOI":"10.1371\/journal.pone.0071462","article-title":"Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data","volume":"8","author":"Y Guo","year":"2013","journal-title":"PLoS ONE"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/nri844","article-title":"BAFF: A fundamental survival factor for B cells","volume":"2","author":"F Mackay","year":"2002","journal-title":"Nat Rev Immunol"}],"updated-by":[{"DOI":"10.1371\/journal.pone.0224062","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2019,10,24]],"date-time":"2019-10-24T00:00:00Z","timestamp":1571875200000}}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0197162","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T20:34:29Z","timestamp":1720298069000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0197162"}},"subtitle":[],"editor":[{"given":"Petr V","family":"Nazarov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,5,16]]},"references-count":36,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2018,5,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0197162","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.pone.0224062","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,5,16]]}}}