{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T18:09:13Z","timestamp":1792001353461,"version":"4.4.0"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,5,13]],"date-time":"2014-05-13T00:00:00Z","timestamp":1399939200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2014,5,13]],"date-time":"2014-05-13T00:00:00Z","timestamp":1399939200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"DOI":"10.1038\/ncomms4850","type":"journal-article","created":{"date-parts":[[2014,5,13]],"date-time":"2014-05-13T10:31:27Z","timestamp":1399977087000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":57,"title":["Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency"],"prefix":"10.1038","volume":"5","author":[{"given":"Fabio","family":"Iannelli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnese","family":"Collino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shruti","family":"Sinha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrico","family":"Radaelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paola","family":"Nicoli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorenzo","family":"D\u2019Antiga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aurelio","family":"Sonzogni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jamila","family":"Faivre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Annick Buendia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekkehard","family":"Sturm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard J.","family":"Thompson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. S.","family":"Knisely","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gioacchino","family":"Natoli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serena","family":"Ghisletti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca D.","family":"Ciccarelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,5,13]]},"reference":[{"key":"BFncomms4850_CR1","doi-asserted-by":"publisher","first-page":"5093","DOI":"10.1038\/sj.onc.1206557","volume":"22","author":"TM Block","year":"2003","unstructured":"Block, T. M., Mehta, A. S., Fimmel, C. J. & Jordan, R. Molecular viral oncology of hepatocellular carcinoma. Oncogene 22, 5093\u20135107 (2003).","journal-title":"Oncogene"},{"key":"BFncomms4850_CR2","doi-asserted-by":"publisher","first-page":"2557","DOI":"10.1053\/j.gastro.2007.04.061","volume":"132","author":"HB El-Serag","year":"2007","unstructured":"El-Serag, H. B. & Rudolph, K. L. Hepatocellular carcinoma: epidemiology and molecular carcinogenesis. Gastroenterology 132, 2557\u20132576 (2007).","journal-title":"Gastroenterology"},{"key":"BFncomms4850_CR3","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1038\/ng.2256","volume":"44","author":"C Guichard","year":"2012","unstructured":"Guichard, C. et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat. Genet. 44, 694\u2013698 (2012).","journal-title":"Nat. Genet."},{"key":"BFncomms4850_CR4","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1038\/ng.2391","volume":"44","author":"J Huang","year":"2012","unstructured":"Huang, J. et al. Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat. Genet. 44, 1117\u20131121 (2012).","journal-title":"Nat. Genet."},{"key":"BFncomms4850_CR5","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1038\/ng.903","volume":"43","author":"M Li","year":"2011","unstructured":"Li, M. et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat. Genet. 43, 828\u2013829 (2011).","journal-title":"Nat. Genet."},{"key":"BFncomms4850_CR6","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1038\/ng.2291","volume":"44","author":"A Fujimoto","year":"2012","unstructured":"Fujimoto, A. et al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat. Genet. 44, 760\u2013764 (2012).","journal-title":"Nat. Genet."},{"key":"BFncomms4850_CR7","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1038\/ng.804","volume":"43","author":"Y Totoki","year":"2011","unstructured":"Totoki, Y. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat. Genet. 43, 464\u2013469 (2011).","journal-title":"Nat. Genet."},{"key":"BFncomms4850_CR8","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1101\/gr.133926.111","volume":"22","author":"Z Jiang","year":"2012","unstructured":"Jiang, Z. et al. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res. 22, 593\u2013601 (2012).","journal-title":"Genome Res."},{"key":"BFncomms4850_CR9","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/286533a0","volume":"286","author":"C Brechot","year":"1980","unstructured":"Brechot, C., Pourcel, C., Louise, A., Rain, B. & Tiollais, P. Presence of integrated hepatitis B virus DNA sequences in cellular DNA of human hepatocellular carcinoma. Nature 286, 533\u2013535 (1980).","journal-title":"Nature"},{"key":"BFncomms4850_CR10","doi-asserted-by":"publisher","first-page":"S26","DOI":"10.1016\/S2210-7401(12)70018-9","volume":"36","author":"E Jacquemin","year":"2012","unstructured":"Jacquemin, E. Progressive familial intrahepatic cholestasis. Clin. Res. Hepatol. Gastroenterol. 36, S26\u2013S35 (2012).","journal-title":"Clin. Res. Hepatol. Gastroenterol."},{"key":"BFncomms4850_CR11","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1002\/hep.21287","volume":"44","author":"AS Knisely","year":"2006","unstructured":"Knisely, A. S. et al. Hepatocellular carcinoma in ten children under five years of age with bile salt export pump deficiency. Hepatology 44, 478\u2013486 (2006).","journal-title":"Hepatology"},{"key":"BFncomms4850_CR12","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1016\/0092-8674(93)90380-9","volume":"75","author":"JJ Smit","year":"1993","unstructured":"Smit, J. J. et al. Homozygous disruption of the murine mdr2 P-glycoprotein gene leads to a complete absence of phospholipid from bile and to liver disease. Cell 75, 451\u2013462 (1993).","journal-title":"Cell"},{"key":"BFncomms4850_CR13","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1053\/j.gastro.2004.04.009","volume":"127","author":"P Fickert","year":"2004","unstructured":"Fickert, P. et al. Regurgitation of bile acids from leaky bile ducts causes sclerosing cholangitis in Mdr2 (Abcb4) knockout mice. Gastroenterology 127, 261\u2013274 (2004).","journal-title":"Gastroenterology"},{"key":"BFncomms4850_CR14","first-page":"1237","volume":"145","author":"TH Mauad","year":"1994","unstructured":"Mauad, T. H. et al. Mice with homozygous disruption of the mdr2 P-glycoprotein gene. A novel animal model for studies of nonsuppurative inflammatory cholangitis and hepatocarcinogenesis. Am. J. Pathol. 145, 1237\u20131245 (1994).","journal-title":"Am. J. Pathol."},{"key":"BFncomms4850_CR15","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/nature02924","volume":"431","author":"E Pikarsky","year":"2004","unstructured":"Pikarsky, E. et al. NF-kappaB functions as a tumour promoter in inflammation-associated cancer. Nature 431, 461\u2013466 (2004).","journal-title":"Nature"},{"key":"BFncomms4850_CR16","doi-asserted-by":"publisher","first-page":"1159","DOI":"10.1158\/1541-7786.MCR-07-0172","volume":"5","author":"M Katzenellenbogen","year":"2007","unstructured":"Katzenellenbogen, M. et al. Molecular mechanisms of liver carcinogenesis in the mdr2-knockout mice. Mol. Cancer Res. 5, 1159\u20131170 (2007).","journal-title":"Mol. Cancer Res."},{"key":"BFncomms4850_CR17","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.1126\/science.1235122","volume":"339","author":"B Vogelstein","year":"2013","unstructured":"Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546\u20131558 (2013).","journal-title":"Science"},{"key":"BFncomms4850_CR18","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1038\/ng.2412","volume":"44","author":"ZGenomic Zhang","year":"2012","unstructured":"Zhang, Z. Genomic. landscape of liver cancer. Nat. Genet. 44, 1075\u20131077 (2012).","journal-title":"Nat. Genet."},{"key":"BFncomms4850_CR19","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/nrc1299","volume":"4","author":"PA Futreal","year":"2004","unstructured":"Futreal, P. A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177\u2013183 (2004).","journal-title":"Nat. Rev. Cancer"},{"key":"BFncomms4850_CR20","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1038\/nature12213","volume":"499","author":"MS Lawrence","year":"2013","unstructured":"Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214\u2013218 (2013).","journal-title":"Nature"},{"key":"BFncomms4850_CR21","doi-asserted-by":"crossref","unstructured":"An, O. et al. NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. Database 2014, (2014).","DOI":"10.1093\/database\/bau015"},{"key":"BFncomms4850_CR22","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1038\/nature08822","volume":"463","author":"R Beroukhim","year":"2010","unstructured":"Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899\u2013905 (2010).","journal-title":"Nature"},{"key":"BFncomms4850_CR23","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.cell.2010.11.055","volume":"144","author":"PJ Stephens","year":"2011","unstructured":"Stephens, P. J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27\u201340 (2011).","journal-title":"Cell"},{"key":"BFncomms4850_CR24","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1016\/j.cell.2013.02.023","volume":"152","author":"JO Korbel","year":"2013","unstructured":"Korbel, J. O. & Campbell, P. J. Criteria for inference of chromothripsis in cancer genomes. Cell 152, 1226\u20131236 (2013).","journal-title":"Cell"},{"key":"BFncomms4850_CR25","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1016\/j.cell.2007.06.009","volume":"129","author":"BD Manning","year":"2007","unstructured":"Manning, B. D. & Cantley, L. C. AKT\/PKB signalling: navigating downstream. Cell 129, 1261\u20131274 (2007).","journal-title":"Cell"},{"key":"BFncomms4850_CR26","doi-asserted-by":"publisher","first-page":"3100","DOI":"10.1038\/sj.onc.1210392","volume":"26","author":"M Raman","year":"2007","unstructured":"Raman, M., Chen, W. & Cobb, M. H. Differential regulation and properties of MAPKs. Oncogene 26, 3100\u20133112 (2007).","journal-title":"Oncogene"},{"key":"BFncomms4850_CR27","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1053\/j.gastro.2006.01.006","volume":"130","author":"DF Calvisi","year":"2006","unstructured":"Calvisi, D. F. et al. Ubiquitous activation of Ras and Jak\/Stat pathways in human HCC. Gastroenterology 130, 1117\u20131128 (2006).","journal-title":"Gastroenterology"},{"key":"BFncomms4850_CR28","doi-asserted-by":"publisher","first-page":"1521","DOI":"10.1053\/j.gastro.2008.02.015","volume":"134","author":"S Yea","year":"2008","unstructured":"Yea, S. et al. Ras promotes growth by alternative splicing-mediated inactivation of the KLF6 tumor suppressor in hepatocellular carcinoma. Gastroenterology 134, 1521\u20131531 (2008).","journal-title":"Gastroenterology"},{"key":"BFncomms4850_CR29","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.1053\/j.gastro.2010.12.006","volume":"140","author":"DF Calvisi","year":"2011","unstructured":"Calvisi, D. F. et al. Increased lipogenesis, induced by AKT-mTORC1-RPS6 signaling, promotes development of human hepatocellular carcinoma. Gastroenterology 140, 1071\u20131083 (2011).","journal-title":"Gastroenterology"},{"key":"BFncomms4850_CR30","doi-asserted-by":"publisher","first-page":"2207","DOI":"10.1073\/pnas.0908867107","volume":"107","author":"H Barash","year":"2010","unstructured":"Barash, H. et al. Accelerated carcinogenesis following liver regeneration is associated with chronic inflammation-induced double-strand DNA breaks. Proc. Natl Acad. Sci. USA 107, 2207\u20132212 (2010).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms4850_CR31","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1083\/jcb.200803042","volume":"181","author":"I Jaco","year":"2008","unstructured":"Jaco, I., Canela, A., Vera, E. & Blasco, M. A. Centromere mitotic recombination in mammalian cells. J. Cell Biol. 181, 885\u2013892 (2008).","journal-title":"J. Cell Biol."},{"key":"BFncomms4850_CR32","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1016\/S0092-8674(00)00116-1","volume":"103","author":"RJ Davis","year":"2000","unstructured":"Davis, R. J. Signal transduction by the JNK group of MAP kinases. Cell 103, 239\u2013252 (2000).","journal-title":"Cell"},{"key":"BFncomms4850_CR33","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1101\/gad.888501","volume":"15","author":"C Tournier","year":"2001","unstructured":"Tournier, C. et al. MKK7 is an essential component of the JNK signal transduction pathway activated by proinflammatory cytokines. Genes Dev. 15, 1419\u20131426 (2001).","journal-title":"Genes Dev."},{"key":"BFncomms4850_CR34","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/ncb1098","volume":"6","author":"T Wada","year":"2004","unstructured":"Wada, T. et al. MKK7 couples stress signalling to G2\/M cell-cycle progression and cellular senescence. Nat. Cell Biol. 6, 215\u2013226 (2004).","journal-title":"Nat. Cell Biol."},{"key":"BFncomms4850_CR35","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.ceb.2007.02.001","volume":"19","author":"CR Weston","year":"2007","unstructured":"Weston, C. R. & Davis, R. J. The JNK signal transduction pathway. Curr.Opin. Cell Biol. 19, 142\u2013149 (2007).","journal-title":"Curr.Opin. Cell Biol."},{"key":"BFncomms4850_CR36","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1016\/j.ccr.2012.04.026","volume":"21","author":"K Nikolaou","year":"2012","unstructured":"Nikolaou, K. et al. Inactivation of the deubiquitinase CYLD in hepatocytes causes apoptosis, inflammation, fibrosis, and cancer. Cancer Cell 21, 738\u2013750 (2012).","journal-title":"Cancer Cell"},{"key":"BFncomms4850_CR37","doi-asserted-by":"publisher","first-page":"10544","DOI":"10.1073\/pnas.0603499103","volume":"103","author":"T Sakurai","year":"2006","unstructured":"Sakurai, T., Maeda, S., Chang, L. & Karin, M. Loss of hepatic NF-kappa B activity enhances chemical hepatocarcinogenesis through sustained c-Jun N-terminal kinase 1 activation. Proc. Natl Acad. Sci. USA 103, 10544\u201310551 (2006).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms4850_CR38","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/ng2033","volume":"39","author":"L Hui","year":"2007","unstructured":"Hui, L. et al. p38alpha suppresses normal and cancer cell proliferation by antagonizing the JNK-c-Jun pathway. Nat. Genet. 39, 741\u2013749 (2007).","journal-title":"Nat. Genet."},{"key":"BFncomms4850_CR39","doi-asserted-by":"publisher","first-page":"3943","DOI":"10.1172\/JCI37156","volume":"118","author":"L Hui","year":"2008","unstructured":"Hui, L., Zatloukal, K., Scheuch, H., Stepniak, E. & Wagner, E. F. Proliferation of human HCC cells and chemically induced mouse liver cancers requires JNK1-dependent p21 downregulation. J. Clin. Invest. 118, 3943\u20133953 (2008).","journal-title":"J. Clin. Invest."},{"key":"BFncomms4850_CR40","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1016\/j.ccr.2009.12.048","volume":"17","author":"G He","year":"2010","unstructured":"He, G. et al. Hepatocyte IKKbeta\/NF-kappaB inhibits tumor promotion and progression by preventing oxidative stress-driven STAT3 activation. Cancer Cell 17, 286\u2013297 (2010).","journal-title":"Cancer Cell"},{"key":"BFncomms4850_CR41","doi-asserted-by":"publisher","first-page":"13681","DOI":"10.1073\/pnas.251194298","volume":"98","author":"BL Bennett","year":"2001","unstructured":"Bennett, B. L. et al. SP600125, an anthrapyrazolone inhibitor of Jun N-terminal kinase. Proc. Natl Acad. Sci. USA 98, 13681\u201313686 (2001).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms4850_CR42","first-page":"29","volume":"8","author":"X Lan","year":"2013","unstructured":"Lan, X. et al. Morphine induces albuminuria by compromising podocyte integrity. PLoS ONE 8, 29 (2013).","journal-title":"PLoS ONE"},{"key":"BFncomms4850_CR43","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1016\/j.ccr.2012.04.026","volume":"21","author":"K Nikolaou","year":"2012","unstructured":"Nikolaou, K. et al. Inactivation of the deubiquitinase CYLD in hepatocytes causes apoptosis, inflammation, fibrosis, and cancer. Cancer Cell 21, 738\u2013750 (2012).","journal-title":"Cancer Cell"},{"key":"BFncomms4850_CR44","doi-asserted-by":"publisher","first-page":"3231","DOI":"10.4049\/jimmunol.1101739","volume":"189","author":"S Shibata","year":"2012","unstructured":"Shibata, S. et al. Adiponectin regulates cutaneous wound healing by promoting keratinocyte proliferation and migration via the ERK signaling pathway. J. Immunol. 189, 3231\u20133241 (2012).","journal-title":"J. Immunol."},{"key":"BFncomms4850_CR45","doi-asserted-by":"publisher","first-page":"1835","DOI":"10.4049\/jimmunol.1203013","volume":"191","author":"Z Tan","year":"2013","unstructured":"Tan, Z. et al. IL-17A plays a critical role in the pathogenesis of liver fibrosis through hepatic stellate cell activation. J. Immunol. 191, 1835\u20131844 (2013).","journal-title":"J. Immunol."},{"key":"BFncomms4850_CR46","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1016\/j.cell.2012.08.034","volume":"151","author":"L Ye","year":"2012","unstructured":"Ye, L. et al. TRPV4 is a regulator of adipose oxidative metabolism, inflammation, and energy homeostasis. Cell 151, 96\u2013110 (2012).","journal-title":"Cell"},{"key":"BFncomms4850_CR47","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1101\/gr.103663.109","volume":"20","author":"M Volker","year":"2010","unstructured":"Volker, M. et al. Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Res. 20, 503\u2013511 (2010).","journal-title":"Genome Res."},{"key":"BFncomms4850_CR48","first-page":"1188","volume":"57","author":"PK Gupta","year":"1997","unstructured":"Gupta, P. K. et al. High frequency in vivo loss of heterozygosity is primarily a consequence of mitotic recombination. Cancer Res. 57, 1188\u20131193 (1997).","journal-title":"Cancer Res."},{"key":"BFncomms4850_CR49","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nature12625","volume":"501","author":"RA Burrell","year":"2013","unstructured":"Burrell, R. A., McGranahan, N., Bartek, J. & Swanton, C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature 501, 338\u2013345 (2013).","journal-title":"Nature"},{"key":"BFncomms4850_CR50","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1038\/nature11935","volume":"494","author":"RA Burrell","year":"2013","unstructured":"Burrell, R. A. et al. Replication stress links structural and numerical cancer chromosomal instability. Nature 494, 492\u2013496 (2013).","journal-title":"Nature"},{"key":"BFncomms4850_CR51","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1016\/j.molonc.2011.05.002","volume":"5","author":"A Dereli-Oz","year":"2011","unstructured":"Dereli-Oz, A., Versini, G. & Halazonetis, T. D. Studies of genomic copy number changes in human cancers reveal signatures of DNA replication stress. Mol. Oncol. 5, 308\u2013314 (2011).","journal-title":"Mol. Oncol."},{"key":"BFncomms4850_CR52","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1038\/ng1861","volume":"38","author":"SL Carter","year":"2006","unstructured":"Carter, S. L., Eklund, A. C., Kohane, I. S., Harris, L. N. & Szallasi, Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat. Genet. 38, 1043\u20131048 (2006).","journal-title":"Nat. Genet."},{"key":"BFncomms4850_CR53","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1056\/NEJMra0910283","volume":"364","author":"HK Eltzschig","year":"2011","unstructured":"Eltzschig, H. K. & Carmeliet, P. Hypoxia and inflammation. New Engl. J. Med. 364, 656\u2013665 (2011).","journal-title":"New Engl. J. Med."},{"key":"BFncomms4850_CR54","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/S1097-2765(00)80137-9","volume":"2","author":"A Coquelle","year":"1998","unstructured":"Coquelle, A., Toledo, F., Stern, S., Bieth, A. & Debatisse, M. A new role for hypoxia in tumor progression: induction of fragile site triggering genomic rearrangements and formation of complex DMs and HSRs. Mol. Cell 2, 259\u2013265 (1998).","journal-title":"Mol. Cell"},{"key":"BFncomms4850_CR55","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1242\/jcs.092262","volume":"125","author":"R Kumareswaran","year":"2012","unstructured":"Kumareswaran, R. et al. Chronic hypoxia compromises repair of DNA double-strand breaks to drive genetic instability. J. Cell Sci. 125, 189\u2013199 (2012).","journal-title":"J. Cell Sci."},{"key":"BFncomms4850_CR56","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1038\/nrc1209","volume":"3","author":"R Eferl","year":"2003","unstructured":"Eferl, R. & Wagner, E. F. AP-1: a double-edged sword in tumorigenesis. Nat. Rev. Cancer 3, 859\u2013868 (2003).","journal-title":"Nat. Rev. Cancer"},{"key":"BFncomms4850_CR57","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1101\/gad.1989311","volume":"25","author":"M Das","year":"2011","unstructured":"Das, M., Garlick, D. S., Greiner, D. L. & Davis, R. J. The role of JNK in the development of hepatocellular carcinoma. Genes Dev. 25, 634\u2013645 (2011).","journal-title":"Genes Dev."},{"key":"BFncomms4850_CR58","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1016\/j.bcp.2007.09.013","volume":"75","author":"Z Dvorak","year":"2008","unstructured":"Dvorak, Z. et al. JNK inhibitor SP600125 is a partial agonist of human aryl hydrocarbon receptor and induces CYP1A1 and CYP1A2 genes in primary human hepatocytes. Biochem. Pharmacol. 75, 580\u2013588 (2008).","journal-title":"Biochem. Pharmacol."},{"key":"BFncomms4850_CR59","doi-asserted-by":"publisher","first-page":"4844","DOI":"10.1128\/JVI.06649-11","volume":"86","author":"S Marozin","year":"2012","unstructured":"Marozin, S. et al. Posttranslational modification of vesicular stomatitis virus glycoprotein, but not JNK inhibition, is the antiviral mechanism of SP600125. J. Virol. 86, 4844\u20134855 (2012).","journal-title":"J. Virol."},{"key":"BFncomms4850_CR60","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"BFncomms4850_CR61","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1101\/gr.129684.111","volume":"22","author":"DC Koboldt","year":"2012","unstructured":"Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568\u2013576 (2012).","journal-title":"Genome Res."},{"key":"BFncomms4850_CR62","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.ygeno.2005.04.008","volume":"86","author":"X Ge","year":"2005","unstructured":"Ge, X. et al. Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics 86, 127\u2013141 (2005).","journal-title":"Genomics"},{"key":"BFncomms4850_CR63","doi-asserted-by":"publisher","first-page":"6062","DOI":"10.1073\/pnas.0400782101","volume":"101","author":"AI Su","year":"2004","unstructured":"Su, A. I. et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA 101, 6062\u20136067 (2004).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms4850_CR64","doi-asserted-by":"publisher","first-page":"16910","DOI":"10.1073\/pnas.1009843107","volume":"107","author":"P Van Loo","year":"2010","unstructured":"Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910\u201316915 (2010).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms4850_CR65","doi-asserted-by":"publisher","first-page":"D793","DOI":"10.1093\/nar\/gks1055","volume":"41","author":"A Kamburov","year":"2013","unstructured":"Kamburov, A., Stelzl, U., Lehrach, H. & Herwig, R. The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res. 41, D793\u2013D800 (2013).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms4850_CR66","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/S0091-679X(08)61797-5","volume":"13","author":"PO Seglen","year":"1976","unstructured":"Seglen, P. O. Preparation of isolated rat liver cells. Methods Cell Biol. 13, 29\u201383 (1976).","journal-title":"Methods Cell Biol."},{"key":"BFncomms4850_CR67","doi-asserted-by":"publisher","first-page":"5S","DOI":"10.1177\/0192623310386499","volume":"38","author":"B Thoolen","year":"2010","unstructured":"Thoolen, B. et al. Proliferative and nonproliferative lesions of the rat and mouse hepatobiliary system. Toxicol. Pathol. 38, 5S\u201381S (2010).","journal-title":"Toxicol. Pathol."},{"key":"BFncomms4850_CR68","doi-asserted-by":"publisher","first-page":"D250","DOI":"10.1093\/nar\/gkm796","volume":"36","author":"LJ Jensen","year":"2008","unstructured":"Jensen, L. J. et al. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 36, D250\u2013D254 (2008).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms4850_CR69","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1101\/gr.114876.110","volume":"21","author":"A Abyzov","year":"2011","unstructured":"Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974\u2013984 (2011).","journal-title":"Genome Res."},{"key":"BFncomms4850_CR70","doi-asserted-by":"publisher","first-page":"R23","DOI":"10.1186\/gb-2009-10-2-r23","volume":"10","author":"JO Korbel","year":"2009","unstructured":"Korbel, J. O. et al. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 10, R23 (2009).","journal-title":"Genome Biol."}],"updated-by":[{"DOI":"10.1038\/ncomms8456","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2015,7,2]],"date-time":"2015-07-02T00:00:00Z","timestamp":1435795200000}}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/ncomms4850.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/ncomms4850","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/ncomms4850.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,6]],"date-time":"2023-01-06T03:51:46Z","timestamp":1672977106000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/ncomms4850"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,13]]},"references-count":70,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2014,9,22]]}},"alternative-id":["BFncomms4850"],"URL":"https:\/\/doi.org\/10.1038\/ncomms4850","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,13]]},"assertion":[{"value":"13 December 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 April 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 July 2015","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Update","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A correction has been published and is appended to both the HTML and PDF versions of this paper. The error has not been fixed in the paper.","order":6,"name":"change_details","label":"Change Details","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":"3850"}}