{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T14:42:29Z","timestamp":1791816149571,"version":"4.3.4"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,11,8]],"date-time":"2016-11-08T00:00:00Z","timestamp":1478563200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,11,8]],"date-time":"2016-11-08T00:00:00Z","timestamp":1478563200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Chromosomal rearrangements are initiating events in acute lymphoblastic leukaemia (ALL). Here using RNA sequencing of 560 ALL cases, we identify rearrangements between<jats:italic>MEF2D<\/jats:italic>(myocyte enhancer factor 2D) and five genes (<jats:italic>BCL9<\/jats:italic>,<jats:italic>CSF1R<\/jats:italic>,<jats:italic>DAZAP1<\/jats:italic>,<jats:italic>HNRNPUL1<\/jats:italic>and<jats:italic>SS18<\/jats:italic>) in 22 B progenitor ALL (B-ALL) cases with a distinct gene expression profile, the most common of which is<jats:italic>MEF2D-BCL9<\/jats:italic>. Examination of an extended cohort of 1,164 B-ALL cases identified 30 cases with<jats:italic>MEF2D<\/jats:italic>rearrangements, which include an additional fusion partner,<jats:italic>FOXJ2<\/jats:italic>; thus,<jats:italic>MEF2D-<\/jats:italic>rearranged cases comprise 5.3% of cases lacking recurring alterations.<jats:italic>MEF2D-<\/jats:italic>rearranged ALL is characterized by a distinct immunophenotype, DNA copy number alterations at the rearrangement sites, older diagnosis age and poor outcome. The rearrangements result in enhanced MEF2D transcriptional activity, lymphoid transformation, activation of<jats:italic>HDAC9<\/jats:italic>expression and sensitive to histone deacetylase inhibitor treatment. Thus,<jats:italic>MEF2D-<\/jats:italic>rearranged ALL represents a distinct form of high-risk leukaemia, for which new therapeutic approaches should be considered.<\/jats:p>","DOI":"10.1038\/ncomms13331","type":"journal-article","created":{"date-parts":[[2016,11,8]],"date-time":"2016-11-08T10:26:19Z","timestamp":1478600779000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":258,"title":["Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia"],"prefix":"10.1038","volume":"7","author":[{"given":"Zhaohui","family":"Gu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"Churchman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"Roberts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongjin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard C.","family":"Harvey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7868-3049","authenticated-orcid":false,"given":"Kelly","family":"McCastlain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shalini C.","family":"Reshmi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debbie","family":"Payne-Turner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilaria","family":"Iacobucci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Shao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I-Ming","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus","family":"Valentine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deqing","family":"Pei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen L.","family":"Mungall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0905-2742","authenticated-orcid":false,"given":"Andrew J.","family":"Mungall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yussanne","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Marra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eileen","family":"Stonerock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie M.","family":"Gastier-Foster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meenakshi","family":"Devidas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunfeng","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brent","family":"Wood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Borowitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric E.","family":"Larsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Maloney","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonard A.","family":"Mattano Jr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Angiolillo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7820-9635","authenticated-orcid":false,"given":"Wanda L.","family":"Salzer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael J.","family":"Burke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Gianni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orietta","family":"Spinelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerald P.","family":"Radich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark D.","family":"Minden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony V.","family":"Moorman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bella","family":"Patel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adele K.","family":"Fielding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob M.","family":"Rowe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Selina M.","family":"Luger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ravi","family":"Bhatia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ibrahim","family":"Aldoss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J.","family":"Forman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Kohlschmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krzysztof","family":"Mr\u00f3zek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guido","family":"Marcucci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara D.","family":"Bloomfield","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wendy","family":"Stock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Kornblau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hagop M.","family":"Kantarjian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Konopleva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Paietta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheryl L.","family":"Willman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mignon","family":"L. Loh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"P. Hunger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1871-1850","authenticated-orcid":false,"given":"Charles G.","family":"Mullighan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,11,8]]},"reference":[{"key":"BFncomms13331_CR1","doi-asserted-by":"publisher","first-page":"3977","DOI":"10.1182\/blood-2015-02-580043","volume":"125","author":"SP Hunger","year":"2015","unstructured":"Hunger, S. P. & Mullighan, C. G. Redefining ALL classification: toward detecting high-risk ALL and implementing precision medicine. Blood 125, 3977\u20133987 (2015).","journal-title":"Blood"},{"key":"BFncomms13331_CR2","doi-asserted-by":"publisher","first-page":"1541","DOI":"10.1056\/NEJMra1400972","volume":"373","author":"SP Hunger","year":"2015","unstructured":"Hunger, S. P. & Mullighan, C. G. Acute lymphoblastic leukemia in children. N. Engl. J. Med. 373, 1541\u20131552 (2015).","journal-title":"N. Engl. J. Med."},{"key":"BFncomms13331_CR3","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1056\/NEJMoa1403088","volume":"371","author":"KG Roberts","year":"2014","unstructured":"Roberts, K. G. et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N. Engl. J. Med. 371, 1005\u20131015 (2014).","journal-title":"N. Engl. J. Med."},{"key":"BFncomms13331_CR4","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/j.blre.2012.01.001","volume":"26","author":"AV Moorman","year":"2012","unstructured":"Moorman, A. V. The clinical relevance of chromosomal and genomic abnormalities in B-cell precursor acute lymphoblastic leukaemia. Blood Rev. 26, 123\u2013135 (2012).","journal-title":"Blood Rev."},{"key":"BFncomms13331_CR5","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1182\/blood.V91.6.1873","volume":"91","author":"TG Willis","year":"1998","unstructured":"Willis, T. G. et al. Molecular cloning of translocation t(1;14)(q21;q32) defines a novel gene (BCL9) at chromosome 1q21. Blood 91, 1873\u20131881 (1998).","journal-title":"Blood"},{"key":"BFncomms13331_CR6","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1182\/blood-2006-10-052282","volume":"110","author":"TL Gu","year":"2007","unstructured":"Gu, T. L. et al. A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia. Blood 110, 323\u2013333 (2007).","journal-title":"Blood"},{"key":"BFncomms13331_CR7","doi-asserted-by":"publisher","first-page":"3012","DOI":"10.1200\/JCO.2014.55.4105","volume":"32","author":"KG Roberts","year":"2014","unstructured":"Roberts, K. G. et al. Outcomes of children with BCR-ABL1-like acute lymphoblastic leukemia treated with risk-directed therapy based on the levels of minimal residual disease. J. Clin. Oncol. 32, 3012\u20133020 (2014).","journal-title":"J. Clin. Oncol."},{"key":"BFncomms13331_CR8","doi-asserted-by":"publisher","first-page":"4874","DOI":"10.1182\/blood-2009-08-239681","volume":"116","author":"RC Harvey","year":"2010","unstructured":"Harvey, R. C. et al. Identification of novel cluster groups in pediatric high-risk B-precursor acute lymphoblastic leukemia with gene expression profiling: correlation with genome-wide DNA copy number alterations, clinical characteristics, and outcome. Blood 116, 4874\u20134884 (2010).","journal-title":"Blood"},{"key":"BFncomms13331_CR9","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1128\/MCB.01415-06","volume":"27","author":"M Haberland","year":"2007","unstructured":"Haberland, M. et al. Regulation of HDAC9 gene expression by MEF2 establishes a negative-feedback loop in the transcriptional circuitry of muscle differentiation. Mol. Cell Biol. 27, 518\u2013525 (2007).","journal-title":"Mol. Cell Biol."},{"key":"BFncomms13331_CR10","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1111\/j.2517-6161.1972.tb00899.x","volume":"34","author":"D Cox","year":"1972","unstructured":"Cox, D. Regression models and life-tables. J. R. Stat. Soc. 34, 187\u2013220 (1972).","journal-title":"J. R. Stat. Soc."},{"key":"BFncomms13331_CR11","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/nature09727","volume":"471","author":"CG Mullighan","year":"2011","unstructured":"Mullighan, C. G. et al. CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471, 235\u2013239 (2011).","journal-title":"Nature"},{"key":"BFncomms13331_CR12","doi-asserted-by":"publisher","first-page":"12249","DOI":"10.1021\/jacs.5b04988","volume":"137","author":"LR Hoggard","year":"2015","unstructured":"Hoggard, L. R. et al. Rational design of selective small-molecule inhibitors for beta-catenin\/B-cell lymphoma 9 protein-protein interactions. J. Am. Chem. Soc. 137, 12249\u201312260 (2015).","journal-title":"J. Am. Chem. Soc."},{"key":"BFncomms13331_CR13","doi-asserted-by":"publisher","first-page":"1410","DOI":"10.1007\/s10495-010-0475-y","volume":"15","author":"Q Yang","year":"2010","unstructured":"Yang, Q. & Mao, Z. Dysregulation of autophagy and Parkinson\u2019s disease: the MEF2D link. Apoptosis 15, 1410\u20131414 (2010).","journal-title":"Apoptosis"},{"key":"BFncomms13331_CR14","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1126\/science.286.5440.785","volume":"286","author":"Z Mao","year":"1999","unstructured":"Mao, Z., Bonni, A., Xia, F., Nadal-Vicens, M. & Greenberg, M. E. Neuronal activity-dependent cell survival mediated by transcription factor MEF2. Science 286, 785\u2013790 (1999).","journal-title":"Science"},{"key":"BFncomms13331_CR15","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/ni1008-1091","volume":"9","author":"TS Heng","year":"2008","unstructured":"Heng, T. S. & Painter, M. W. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091\u20131094 (2008).","journal-title":"Nat. Immunol."},{"key":"BFncomms13331_CR16","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1182\/blood-2015-04-643270","volume":"127","author":"J Herglotz","year":"2016","unstructured":"Herglotz, J. et al. Essential control of early B-cell development by Mef2 transcription factors. Blood 127, 572\u2013581 (2016).","journal-title":"Blood"},{"key":"BFncomms13331_CR17","first-page":"575","volume":"10","author":"ML Silva","year":"1996","unstructured":"Silva, M. L. et al. Establishment of a new human pre-B leukemia cell line (CEMO-1) with the translocation (1;14)(q21;q32). Leukemia 10, 575\u2013577 (1996).","journal-title":"Leukemia"},{"key":"BFncomms13331_CR18","doi-asserted-by":"publisher","first-page":"1490","DOI":"10.1182\/blood-2009-09-235986","volume":"115","author":"MJ Dyer","year":"2009","unstructured":"Dyer, M. J. et al. Immunoglobulin heavy chain (IGH) locus chromosomal translocations in B-cell precursor acute lymphoblastic leukemia (BCP-ALL): rare clinical curios or potent genetic drivers? Blood 115, 1490\u20131499 (2009).","journal-title":"Blood"},{"key":"BFncomms13331_CR19","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1182\/blood-2009-03-208397","volume":"114","author":"LJ Russell","year":"2009","unstructured":"Russell, L. J. et al. Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia. Blood 114, 2688\u20132698 (2009).","journal-title":"Blood"},{"key":"BFncomms13331_CR20","doi-asserted-by":"publisher","first-page":"1243","DOI":"10.1038\/ng.469","volume":"41","author":"CG Mullighan","year":"2009","unstructured":"Mullighan, C. G. et al. Rearrangement of CRLF2 in B-progenitor- and Down syndrome-associated acute lymphoblastic leukemia. Nat. Genet. 41, 1243\u20131246 (2009).","journal-title":"Nat. Genet."},{"key":"BFncomms13331_CR21","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1016\/j.ccell.2015.12.013","volume":"29","author":"I Iacobucci","year":"2016","unstructured":"Iacobucci, I. et al. Truncating erythropoietin receptor rearrangements in acute lymphoblastic leukemia. Cancer Cell 29, 186\u2013200 (2016).","journal-title":"Cancer Cell"},{"key":"BFncomms13331_CR22","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1016\/j.molcel.2006.09.001","volume":"24","author":"J Sampietro","year":"2006","unstructured":"Sampietro, J. et al. Crystal structure of a \u03b2-catenin\/BCL9\/Tcf4 complex. Mol. Cell 24, 293\u2013300 (2006).","journal-title":"Mol. Cell"},{"key":"BFncomms13331_CR23","doi-asserted-by":"publisher","first-page":"4042","DOI":"10.1158\/1078-0432.CCR-06-2316","volume":"13","author":"M Katoh","year":"2007","unstructured":"Katoh, M. & Katoh, M. WNT signaling pathway and stem cell signaling network. Clin. Cancer Res. 13, 4042\u20134045 (2007).","journal-title":"Clin. Cancer Res."},{"key":"BFncomms13331_CR24","doi-asserted-by":"publisher","first-page":"7577","DOI":"10.1158\/0008-5472.CAN-09-0773","volume":"69","author":"M Mani","year":"2009","unstructured":"Mani, M. et al. BCL9 promotes tumor progression by conferring enhanced proliferative, metastatic, and angiogenic properties to cancer cells. Cancer Res. 69, 7577\u20137586 (2009).","journal-title":"Cancer Res."},{"key":"BFncomms13331_CR25","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1016\/j.bbrc.2009.01.166","volume":"380","author":"HT Yang","year":"2009","unstructured":"Yang, H. T., Peggie, M., Cohen, P. & Rousseau, S. DAZAP1 interacts via its RNA-recognition motifs with the C-termini of other RNA-binding proteins. Biochem. Biophys. Res. Commun. 380, 705\u2013709 (2009).","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"BFncomms13331_CR26","doi-asserted-by":"publisher","first-page":"806","DOI":"10.1038\/sj.leu.2403684","volume":"19","author":"V Prima","year":"2005","unstructured":"Prima, V. et al. Cloning and functional characterization of MEF2D\/DAZAP1 and DAZAP1\/MEF2D fusion proteins created by a variant t(1;19)(q23;p13.3) in acute lymphoblastic leukemia. Leukemia 19, 806\u2013813 (2005).","journal-title":"Leukemia"},{"key":"BFncomms13331_CR27","doi-asserted-by":"publisher","first-page":"2470","DOI":"10.1038\/sj.leu.2404962","volume":"21","author":"V Prima","year":"2007","unstructured":"Prima, V. & Hunger, S. P. Cooperative transformation by MEF2D\/DAZAP1 and DAZAP1\/MEF2D fusion proteins generated by the variant t(1;19) in acute lymphoblastic leukemia. Leukemia 21, 2470\u20132475 (2007).","journal-title":"Leukemia"},{"key":"BFncomms13331_CR28","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1016\/j.molcel.2011.12.035","volume":"45","author":"SE Polo","year":"2012","unstructured":"Polo, S. E. et al. Regulation of DNA-end resection by hnRNPU-like proteins promotes DNA double-strand break signaling and repair. Mol. Cell 45, 505\u2013516 (2012).","journal-title":"Mol. Cell"},{"key":"BFncomms13331_CR29","doi-asserted-by":"publisher","first-page":"e0142991","DOI":"10.1371\/journal.pone.0142991","volume":"10","author":"S Tamaki","year":"2015","unstructured":"Tamaki, S. et al. SS18-SSX, the oncogenic fusion protein in synovial sarcoma, is a cellular context-dependent epigenetic modifier. PLoS ONE 10, e0142991 (2015).","journal-title":"PLoS ONE"},{"key":"BFncomms13331_CR30","doi-asserted-by":"publisher","first-page":"5006","DOI":"10.1038\/onc.2013.443","volume":"33","author":"M Trautmann","year":"2014","unstructured":"Trautmann, M. et al. SS18-SSX fusion protein-induced Wnt\/beta-catenin signaling is a therapeutic target in synovial sarcoma. Oncogene 33, 5006\u20135016 (2014).","journal-title":"Oncogene"},{"key":"BFncomms13331_CR31","doi-asserted-by":"publisher","first-page":"2449","DOI":"10.3892\/ijo.2015.2957","volume":"46","author":"Y Qiang","year":"2015","unstructured":"Qiang, Y. et al. Abnormal expression of Forkhead Box J2 (FOXJ2) suppresses migration and invasion in extrahepatic cholangiocarcinoma and is associated with prognosis. Int. J. Oncol. 46, 2449\u20132458 (2015).","journal-title":"Int. J. Oncol."},{"key":"BFncomms13331_CR32","doi-asserted-by":"publisher","first-page":"2729","DOI":"10.1002\/jcb.24146","volume":"113","author":"Y Wang","year":"2012","unstructured":"Wang, Y. et al. Overexpression of forkhead box J2 can decrease the migration of breast cancer cells. J. Cell Biochem. 113, 2729\u20132737 (2012).","journal-title":"J. Cell Biochem."},{"key":"BFncomms13331_CR33","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"BFncomms13331_CR34","doi-asserted-by":"crossref","unstructured":"Nicorici, D. et al. Fusion Catcher-a tool for finding somatic fusion genes in paired-end RNA-sequencing data.. Preprint at bioRxiv http:\/\/dx.doi.org\/10.1101\/011650 (2014).","DOI":"10.1101\/011650"},{"key":"BFncomms13331_CR35","doi-asserted-by":"publisher","first-page":"R6","DOI":"10.1186\/gb-2011-12-1-r6","volume":"12","author":"H Edgren","year":"2011","unstructured":"Edgren, H. et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol. 12, R6 (2011).","journal-title":"Genome Biol."},{"key":"BFncomms13331_CR36","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders, S., Pyl, P. T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166\u2013169 (2015).","journal-title":"Bioinformatics"},{"key":"BFncomms13331_CR37","doi-asserted-by":"publisher","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","volume":"11","author":"S Anders","year":"2010","unstructured":"Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).","journal-title":"Genome Biol."},{"key":"BFncomms13331_CR38","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545\u201315550 (2005).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms13331_CR39","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"W Huang da","year":"2009","unstructured":"Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44\u201357 (2009).","journal-title":"Nat. Protoc."},{"key":"BFncomms13331_CR40","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297\u20131303 (2010).","journal-title":"Genome Res."},{"key":"BFncomms13331_CR41","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/j.ccr.2012.06.005","volume":"22","author":"KG Roberts","year":"2012","unstructured":"Roberts, K. G. et al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell 22, 153\u2013166 (2012).","journal-title":"Cancer Cell"},{"key":"BFncomms13331_CR42","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1056\/NEJMoa0808253","volume":"360","author":"CG Mullighan","year":"2009","unstructured":"Mullighan, C. G. et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N. Engl J. Med. 360, 470\u2013480 (2009).","journal-title":"N. Engl J. Med."},{"key":"BFncomms13331_CR43","first-page":"163","volume":"50","author":"N Mantel","year":"1966","unstructured":"Mantel, N. Evaluation of survival data and two new rank order statistics arising in its consideration. Cancer Chemother. Rep. 50, 163\u2013170 (1966).","journal-title":"Cancer Chemother. Rep."},{"key":"BFncomms13331_CR44","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1080\/01621459.1999.10474144","volume":"94","author":"JP Fine","year":"1999","unstructured":"Fine, J. P. & Gray, R. J. A proportional hazards model for the subdistribution of a competing risk. J. Am. Stat. Assoc. 94, 496\u2013509 (1999).","journal-title":"J. Am. Stat. Assoc."},{"key":"BFncomms13331_CR45","unstructured":"R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https:\/\/www.R-project.org\/ (2016)."}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/ncomms13331.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/ncomms13331","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/ncomms13331.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,20]],"date-time":"2024-06-20T12:36:06Z","timestamp":1718886966000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/ncomms13331"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,11,8]]},"references-count":45,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12,23]]}},"alternative-id":["BFncomms13331"],"URL":"https:\/\/doi.org\/10.1038\/ncomms13331","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,11,8]]},"assertion":[{"value":"7 February 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 September 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"13331"}}