{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,24]],"date-time":"2025-07-24T11:16:07Z","timestamp":1753355767877},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2013,11,4]],"date-time":"2013-11-04T00:00:00Z","timestamp":1383523200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0076287","type":"journal-article","created":{"date-parts":[[2013,11,4]],"date-time":"2013-11-04T22:16:47Z","timestamp":1383603407000},"page":"e76287","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["Massive Transcriptional Perturbation in Subgroups of Diffuse Large B-Cell Lymphomas"],"prefix":"10.1371","volume":"8","author":[{"given":"Maciej","family":"Rosolowski","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00fcrgen","family":"L\u00e4uter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitriy","family":"Abramov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hans G.","family":"Drexler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Hummel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolfram","family":"Klapper","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roderick A.F.","family":"MacLeod","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shoji","family":"Pellissery","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Friedemann","family":"Horn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reiner","family":"Siebert","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Loeffler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2013,11,4]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/35000501","article-title":"Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling","volume":"403","author":"AA Alizadeh","year":"2000","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1056\/NEJMoa012914","article-title":"The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma","volume":"346","author":"A Rosenwald","year":"2002","journal-title":"N Engl J Med"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1182\/blood-2004-07-2947","article-title":"Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response","volume":"105","author":"S Monti","year":"2005","journal-title":"Blood"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1056\/NEJMoa055351","article-title":"A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling","volume":"354","author":"M Hummel","year":"2006","journal-title":"N Engl J Med"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"2431","DOI":"10.1056\/NEJMoa055759","article-title":"Molecular diagnosis of Burkitt's lymphoma","volume":"354","author":"SS Dave","year":"2006","journal-title":"N Engl J Med"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1038\/leu.2008.166","article-title":"Pathway activation patterns in diffuse large B-cell lymphomas","volume":"22","author":"S Bentink","year":"2008","journal-title":"Leukemia"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1038\/ng.2469","article-title":"Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing","volume":"44","author":"J Richter","year":"2012","journal-title":"Nat Genet"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1038\/ng.2468","article-title":"The genetic landscape of mutations in Burkitt lymphoma","volume":"44","author":"C Love","year":"2012","journal-title":"Nat Genet"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nature11378","article-title":"Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics","volume":"490","author":"R Schmitz","year":"2012","journal-title":"Nature"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1038\/nature10351","article-title":"Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma","volume":"476","author":"RD Morin","year":"2011","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1038\/ng.892","article-title":"Analysis of the coding genome of diffuse large B-cell lymphoma","volume":"43","author":"L Pasqualucci","year":"2011","journal-title":"Nat Genet"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"3879","DOI":"10.1073\/pnas.1121343109","article-title":"Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing","volume":"109","author":"JG Lohr","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"13520","DOI":"10.1073\/pnas.0804295105","article-title":"Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways","volume":"105","author":"G Lenz","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0092-8674(00)81683-9","article-title":"The hallmarks of cancer","volume":"100","author":"D Hanahan","year":"2000","journal-title":"Cell"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1182\/blood-2011-10-388470","article-title":"Patient age at diagnosis is associated with the molecular characteristics of diffuse large B-cell lymphoma","volume":"119","author":"W Klapper","year":"2012","journal-title":"Blood"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/msb.2011.28","article-title":"RNA sequencing reveals two major classes of gene expression levels in metazoan cells","volume":"7","author":"D Hebenstreit","year":"2011","journal-title":"Mol Syst Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/nature09730","article-title":"Inactivating mutations of acetyltransferase genes in B-cell lymphoma","volume":"471","author":"L Pasqualucci","year":"2011","journal-title":"Nature"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/ng.518","article-title":"Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin","volume":"42","author":"RD Morin","year":"2010","journal-title":"Nat Genet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1093\/biomet\/58.3.453","article-title":"The biplot graphical display of matrices with applications to principal compontent analysis","volume":"58","author":"KR Gabriel","year":"1971","journal-title":"Biometrika"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"2313","DOI":"10.1056\/NEJMoa0802885","article-title":"Stromal gene signatures in large-B-cell lymphomas","volume":"359","author":"G Lenz","year":"2008","journal-title":"N Engl J Med"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1056\/NEJMoa041869","article-title":"Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating immune cells","volume":"351","author":"SS Dave","year":"2004","journal-title":"N Engl J Med"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1038\/nature05186","article-title":"Co-evolution of transcriptional and post-translational cell-cycle regulation","volume":"443","author":"LJ Jensen","year":"2006","journal-title":"Nature"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1091\/mbc.02-02-0030","article-title":"Identification of genes periodically expressed in the human cell cycle and their expression in tumors","volume":"13","author":"ML Whitfield","year":"2002","journal-title":"Mol Biol Cell"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1016\/j.molcel.2009.11.016","article-title":"Revealing global regulatory perturbations across human cancers","volume":"36","author":"H Goodarzi","year":"2009","journal-title":"Mol Cell"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1002\/bimj.200800207","article-title":"High-dimensional data analysis: selection of variables, data compression and graphics\u2013application to gene expression","volume":"51","author":"J L\u00e4uter","year":"2009","journal-title":"Biom J"},{"key":"ref26","unstructured":"L\u00e4uter J, Rosolowski M, Glimm E (2012) Exact multivariate tests \u2013 a new effective principle of controlled model choice. arXiv:12022045v1 [statME]."},{"key":"ref27","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.ccr.2012.06.012","article-title":"Synergy between PI3K Signaling and MYC in Burkitt Lymphomagenesis","volume":"22","author":"S Sander","year":"2012","journal-title":"Cancer Cell"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/j.ccr.2012.08.014","article-title":"Metabolic signatures uncover distinct targets in molecular subsets of diffuse large B cell lymphoma","volume":"22","author":"P Caro","year":"2012","journal-title":"Cancer Cell"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.cell.2012.08.026","article-title":"Transcriptional amplification in tumor cells with elevated c-Myc","volume":"151","author":"CY Lin","year":"2012","journal-title":"Cell"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.cell.2012.08.033","article-title":"c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells","volume":"151","author":"Z Nie","year":"2012","journal-title":"Cell"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1182\/blood-2008-01-136465","article-title":"Molecular profiling of pediatric mature B-cell lymphoma treated in population-based prospective clinical trials","volume":"112","author":"W Klapper","year":"2008","journal-title":"Blood"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1182\/blood-2011-01-330795","article-title":"Translocations activating IRF4 identify a subtype of germinal center-derived B-cell lymphoma affecting predominantly children and young adults","volume":"118","author":"I Salaverria","year":"2011","journal-title":"Blood"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1160\/ME9064","article-title":"Development and implementation of an analysis tool for array-based comparative genomic hybridization","volume":"46","author":"M Kreuz","year":"2007","journal-title":"Methods Inf Med"},{"key":"ref34","doi-asserted-by":"crossref","unstructured":"Drexler HG (2010) Guide to Leukemia-Lymphoma Cell Lines. Braunschweig.","DOI":"10.1111\/j.1749-0774.2010.00087.x"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"S96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","article-title":"Variance stabilization applied to microarray data calibration and to the quantification of differential expression","volume":"18","author":"W Huber","year":"2002","journal-title":"Bioinformatics"},{"key":"ref36","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":"ref37","doi-asserted-by":"crossref","first-page":"e22","DOI":"10.1371\/journal.pcbi.0040022","article-title":"Microarray based diagnosis profits from better documentation of gene expression signatures","volume":"4","author":"D Kostka","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"ref38","doi-asserted-by":"crossref","unstructured":"Kaufman L, Rousseeuw PJ (1990) Finding Groups in Data: An Introduction to Cluster Analysis. New Yourk: John Wiley & Sons.","DOI":"10.1002\/9780470316801"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: A graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"PJ Rousseeuw","year":"1987","journal-title":"J Comput Appl Math"},{"key":"ref40","unstructured":"R Development Core Team (2010) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing."},{"key":"ref41","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: Open software development for computational biology and bioinformatics","volume":"5","author":"RC Gentleman","year":"2004","journal-title":"Genome Biology"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0076287","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,1]],"date-time":"2019-08-01T00:29:21Z","timestamp":1564619361000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0076287"}},"subtitle":[],"editor":[{"given":"Ken","family":"Mills","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2013,11,4]]},"references-count":41,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2013,11,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0076287","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,11,4]]}}}