{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,26]],"date-time":"2026-07-26T22:35:41Z","timestamp":1785105341230,"version":"3.55.0"},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"7407","license":[{"start":{"date-parts":[[2012,7,18]],"date-time":"2012-07-18T00:00:00Z","timestamp":1342569600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"},{"start":{"date-parts":[[2012,7,18]],"date-time":"2012-07-18T00:00:00Z","timestamp":1342569600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2012,7,19]]},"DOI":"10.1038\/nature11252","type":"journal-article","created":{"date-parts":[[2012,7,17]],"date-time":"2012-07-17T09:01:56Z","timestamp":1342515716000},"page":"330-337","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7663,"title":["Comprehensive molecular characterization of human colon and rectal cancer"],"prefix":"10.1038","volume":"487","author":[{"name":"The Cancer Genome Atlas Network","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2012,7,18]]},"reference":[{"key":"BFnature11252_CR1","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature07385","volume":"455","author":"The Cancer Genome Atlas Research Ne","year":"2008","unstructured":"The Cancer Genome Atlas Research Network . Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061\u20131068 (2008)","journal-title":"Nature"},{"key":"BFnature11252_CR2","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1038\/nature10166","volume":"474","author":"The Cancer Genome Atlas Research Ne","year":"2011","unstructured":"The Cancer Genome Atlas Research Network . Integrated genomic analyses of ovarian carcinoma. Nature 474, 609\u2013615 (2011)","journal-title":"Nature"},{"key":"BFnature11252_CR3","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1146\/annurev-pathol-011110-130235","volume":"6","author":"ER Fearon","year":"2011","unstructured":"Fearon, E. R. Molecular genetics of colorectal cancer. Annu. Rev. Pathol. 6, 479\u2013507 (2011)","journal-title":"Annu. Rev. Pathol."},{"key":"BFnature11252_CR4","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1038\/ng.936","volume":"43","author":"AJ Bass","year":"2011","unstructured":"Bass, A. J. et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A\u2013TCF7L2 fusion. Nature Genet. 43, 964\u2013968 (2011)","journal-title":"Nature Genet."},{"key":"BFnature11252_CR5","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1126\/science.1133427","volume":"314","author":"T Sjoblom","year":"2006","unstructured":"Sjoblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268\u2013274 (2006)","journal-title":"Science"},{"key":"BFnature11252_CR6","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1126\/science.1145720","volume":"318","author":"LD Wood","year":"2007","unstructured":"Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108\u20131113 (2007)","journal-title":"Science"},{"key":"BFnature11252_CR7","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1093\/jnci\/djh034","volume":"96","author":"A Umar","year":"2004","unstructured":"Umar, A. et al. Revised Bethesda guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability. J. Natl Cancer Inst. 96, 261\u2013268 (2004)","journal-title":"J. Natl Cancer Inst."},{"key":"BFnature11252_CR8","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1126\/science.8484121","volume":"260","author":"LA Aaltonen","year":"1993","unstructured":"Aaltonen, L. A. et al. Clues to the pathogenesis of familial colorectal cancer 260, Science. 812\u2013816 (1993)","journal-title":"Science"},{"key":"BFnature11252_CR9","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1038\/363558a0","volume":"363","author":"Y Ionov","year":"1993","unstructured":"Ionov, Y., Peinado, M. A., Malkhosyan, S., Shibata, D. & Perucho, M. Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis. Nature 363, 558\u2013561 (1993)","journal-title":"Nature"},{"key":"BFnature11252_CR10","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1016\/0092-8674(93)90331-J","volume":"75","author":"R Parsons","year":"1993","unstructured":"Parsons, R. et al. Hypermutability and mismatch repair deficiency in RER+ tumor cells. Cell 75, 1227\u20131236 (1993)","journal-title":"Cell"},{"key":"BFnature11252_CR11","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1101\/gad.2046711","volume":"25","author":"AL Dooley","year":"2011","unstructured":"Dooley, A. L. et al. Nuclear factor I\/B is an oncogene in small cell lung cancer. Genes Dev. 25, 1470\u20131475 (2011)","journal-title":"Genes Dev."},{"key":"BFnature11252_CR12","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1126\/science\/1141515","volume":"316","author":"MB Major","year":"2007","unstructured":"Major, M. B. et al. Wilms tumor suppressor WTX negatively regulates WNT\/\u03b2-catenin signaling. Science 316, 1043\u20131046 (2007)","journal-title":"Science"},{"key":"BFnature11252_CR13","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1053\/j.gastro.2007.05.020","volume":"133","author":"Y Mori-Akiyama","year":"2007","unstructured":"Mori-Akiyama, Y. et al. SOX9 is required for the differentiation of paneth cells in the intestinal epithelium. Gastroenterology 133, 539\u2013546 (2007)","journal-title":"Gastroenterology"},{"key":"BFnature11252_CR14","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1083\/jcb.200704152","volume":"178","author":"P Bastide","year":"2007","unstructured":"Bastide, P. et al. Sox9 regulates cell proliferation and is required for Paneth cell differentiation in the intestinal epithelium. J. Cell Biol. 178, 635\u2013648 (2007)","journal-title":"J. Cell Biol."},{"key":"BFnature11252_CR15","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1002\/humu.21633","volume":"33","author":"S Jones","year":"2012","unstructured":"Jones, S. et al. Somatic mutations in the chromatin remodeling gene ARID1A occur in several tumor types. Hum. Mutat. 33, 100\u2013103 (2012)","journal-title":"Hum. Mutat."},{"key":"BFnature11252_CR16","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/nrc3068","volume":"11","author":"BG Wilson","year":"2011","unstructured":"Wilson, B. G. & Roberts, C. W. SWI\/SNF nucleosome remodellers and cancer. Nat. Rev. Cancer 11, 481\u2013492 (2011)","journal-title":"Nat. Rev. Cancer"},{"key":"BFnature11252_CR17","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1053\/j.seminoncol.2011.05.008","volume":"38","author":"BD Minsky","year":"2011","unstructured":"Minsky, B. D. Unique considerations in the patient with rectal cancer. Semin. Oncol. 38, 542\u2013551 (2011)","journal-title":"Semin. Oncol."},{"key":"BFnature11252_CR18","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1101\/gr.117523.110","volume":"22","author":"T Hinoue","year":"2012","unstructured":"Hinoue, T. et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res. 22, 271\u2013282 (2012)","journal-title":"Genome Res."},{"key":"BFnature11252_CR19","doi-asserted-by":"crossref","first-page":"20007","DOI":"10.1073\/pnas.0710052104","volume":"104","author":"R Beroukhim","year":"2007","unstructured":"Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl Acad. Sci. USA 104, 20007\u201320012 (2007)","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnature11252_CR20","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1002\/gcc.20699","volume":"48","author":"J Camps","year":"2009","unstructured":"Camps, J. et al. Integrative genomics reveals mechanisms of copy number alterations responsible for transcriptional deregulation in colorectal cancer. Genes Chromosom. Cancer 48, 1002\u20131017 (2009)","journal-title":"Genes Chromosom. Cancer"},{"key":"BFnature11252_CR21","first-page":"423","volume":"1","author":"JM Varley","year":"1987","unstructured":"Varley, J. M., Swallow, J. E., Brammar, W. J., Whittaker, J. L. & Walker, R. A. Alterations to either c-erbB-2(neu) or c-myc proto-oncogenes in breast carcinomas correlate with poor short-term prognosis. Oncogene 1, 423\u2013430 (1987)","journal-title":"Oncogene"},{"key":"BFnature11252_CR22","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1016\/S0140-6736(86)91782-4","volume":"327","author":"J Yokota","year":"1986","unstructured":"Yokota, J. et al. Amplification of c-erbB-2 oncogene in human adenocarcinomas in vivo. Lancet 327, 765\u2013767 (1986)","journal-title":"Lancet"},{"key":"BFnature11252_CR23","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1016\/j.cell.2009.01.031","volume":"136","author":"LG van der Flier","year":"2009","unstructured":"van der Flier, L. G. et al. Transcription factor achaete scute-like 2 controls intestinal stem cell fate. Cell 136, 903\u2013912 (2009)","journal-title":"Cell"},{"key":"BFnature11252_CR24","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1136\/gut.2010.231746","volume":"60","author":"AM Jubb","year":"2011","unstructured":"Jubb, A. M., Hoeflich, K. P., Haverty, P. M., Wang, J. & Koeppen, H. Ascl2 and 11p15.5 amplification in colorectal cancer. Gut 60, 1606\u20131607 (2011)","journal-title":"Gut"},{"key":"BFnature11252_CR25","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1136\/gut.2009.195701","volume":"59","author":"DE Stange","year":"2010","unstructured":"Stange, D. E. et al. Expression of an ASCL2 related stem cell signature and IGF2 in colorectal cancer liver metastases with 11p15.5 gain. Gut 59, 1236\u20131244 (2010)","journal-title":"Gut"},{"key":"BFnature11252_CR26","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1126\/science.1080902","volume":"299","author":"H Cui","year":"2003","unstructured":"Cui, H. et al. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science 299, 1753\u20131755 (2003)","journal-title":"Science"},{"key":"BFnature11252_CR27","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1073\/pnas.98.2.591","volume":"98","author":"H Nakagawa","year":"2001","unstructured":"Nakagawa, H. et al. Loss of imprinting of the insulin-like growth factor II gene occurs by biallelic methylation in a core region of H19-associated CTCF-binding sites in colorectal cancer. Proc. Natl Acad. Sci. USA 98, 591\u2013596 (2001)","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnature11252_CR28","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1158\/0008-5472.CAN-09-4456","volume":"70","author":"A Veronese","year":"2010","unstructured":"Veronese, A. et al. Oncogenic role of miR-483-3p at the IGF2\/483 locus. Cancer Res. 70, 3140\u20133149 (2010)","journal-title":"Cancer Res."},{"key":"BFnature11252_CR29","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1101\/gr.125567.111","volume":"22","author":"G Ciriello","year":"2012","unstructured":"Ciriello, G., Cerami, E., Sander, C. & Schultz, N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 22, 398\u2013406 (2012)","journal-title":"Genome Res."},{"key":"BFnature11252_CR30","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/j.cell.2011.03.035","volume":"145","author":"CA Brady","year":"2011","unstructured":"Brady, C. A. et al. Distinct p53 transcriptional programs dictate acute DNA-damage responses and tumor suppression. Cell 145, 571\u2013583 (2011)","journal-title":"Cell"},{"key":"BFnature11252_CR31","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1126\/science.1137509","volume":"315","author":"MN Rivera","year":"2007","unstructured":"Rivera, M. N. et al. An X chromosome gene, WTX, is commonly inactivated in Wilms tumor. Science 315, 642\u2013645 (2007)","journal-title":"Science"},{"key":"BFnature11252_CR32","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1186\/1471-2407-10-413","volume":"10","author":"SK Scheel","year":"2010","unstructured":"Scheel, S. K. et al. Mutations in the WTX-gene are found in some high-grade microsatellite instable (MSI-H) colorectal cancers. BMC Cancer 10, 413 (2010)","journal-title":"BMC Cancer"},{"key":"BFnature11252_CR33","unstructured":"Forbes, S. A. et al. The catalogue of somatic mutations in cancer (COSMIC). Curr. Protoc. Hum. Genet. Ch. 10, Unit 10.11. (2008)"},{"key":"BFnature11252_CR34","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/S0092-8674(00)00121-5","volume":"103","author":"J Massagu\u00e9","year":"2000","unstructured":"Massagu\u00e9, J., Blain, S. W. & Lo, R. S. TGF\u03b2 signaling in growth control, cancer, and heritable disorders. Cell 103, 295\u2013309 (2000)","journal-title":"Cell"},{"key":"BFnature11252_CR35","doi-asserted-by":"crossref","first-page":"i237","DOI":"10.1093\/bioinformatics\/btq182","volume":"26","author":"CJ Vaske","year":"2010","unstructured":"Vaske, C. J. et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 26, i237\u2013i245 (2010)","journal-title":"Bioinformatics"},{"key":"BFnature11252_CR36","doi-asserted-by":"crossref","first-page":"6957","DOI":"10.1158\/0008-5472.CAN-10-1169","volume":"70","author":"CD House","year":"2010","unstructured":"House, C. D. et al. Voltage-gated Na+ channel SCN5A is a key regulator of a gene transcriptional network that controls colon cancer invasion. Cancer Res. 70, 6957\u20136967 (2010)","journal-title":"Cancer Res."},{"key":"BFnature11252_CR37","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1158\/1541-7786.21.3.1","volume":"3","author":"Z Liu","year":"2005","unstructured":"Liu, Z., Lu, H., Jiang, Z., Pastuszyn, A. & Hu, C. A. Apolipoprotein l6, a novel proapoptotic Bcl-2 homology 3-only protein, induces mitochondria-mediated apoptosis in cancer cells. Mol. Cancer Res. 3, 21\u201331 (2005)","journal-title":"Mol. Cancer Res."},{"key":"BFnature11252_CR38","doi-asserted-by":"crossref","first-page":"3323","DOI":"10.1074\/jbc.M808048200","volume":"284","author":"L Topol","year":"2009","unstructured":"Topol, L., Chen, W., Song, H., Day, T. F. & Yang, Y. Sox9 inhibits Wnt signaling by promoting \u03b2-catenin phosphorylation in the nucleus. J. Biol. Chem. 284, 3323\u20133333 (2009)","journal-title":"J. Biol. Chem."},{"key":"BFnature11252_CR39","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1158\/0008-5472.CAN-05-3427","volume":"66","author":"NG Nagl Jr","year":"2006","unstructured":"Nagl, N. G., Jr, Zweitzig, D. R., Thimmapaya, B., Beck, G. R., Jr & Moran, E. The c-myc gene is a direct target of mammalian SWI\/SNF-related complexes during differentiation-associated cell cycle arrest. Cancer Res. 66, 1289\u20131293 (2006)","journal-title":"Cancer Res."},{"key":"BFnature11252_CR40","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/nchembio.137","volume":"5","author":"B Chen","year":"2009","unstructured":"Chen, B. et al. Small molecule-mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer. Nat. Chem. Biol. 5, 100\u2013107 (2009)","journal-title":"Nat. Chem. Biol."},{"key":"BFnature11252_CR41","doi-asserted-by":"crossref","first-page":"5963","DOI":"10.1158\/0008-5472.CAN-10-1028","volume":"70","author":"K Ewan","year":"2010","unstructured":"Ewan, K. et al. A useful approach to identify novel small-molecule inhibitors of Wnt-dependent transcription. Cancer Res. 70, 5963\u20135973 (2010)","journal-title":"Cancer Res."},{"key":"BFnature11252_CR42","doi-asserted-by":"crossref","first-page":"3344","DOI":"10.1091\/mbc.e10-09-0739","volume":"22","author":"U Sack","year":"2011","unstructured":"Sack, U. et al. S100A4-induced cell motility and metastasis is restricted by the Wnt\/\u03b2-catenin pathway inhibitor calcimycin in colon cancer cells. Mol. Biol. Cell 22, 3344\u20133354 (2011)","journal-title":"Mol. Biol. Cell"},{"key":"BFnature11252_CR43","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1363","volume":"6","author":"K Chen","year":"2009","unstructured":"Chen, K. et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods 6, 677\u2013681 (2009)","journal-title":"Nature Methods"},{"key":"BFnature11252_CR44","doi-asserted-by":"crossref","first-page":"E1128","DOI":"10.1073\/pnas.1110574108","volume":"108","author":"R Xi","year":"2011","unstructured":"Xi, R. et al. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc. Natl Acad. Sci. USA 108, E1128\u2013E1136 (2011)","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nature11252.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nature11252","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nature11252.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T06:44:40Z","timestamp":1687589080000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nature11252"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,7,18]]},"references-count":44,"journal-issue":{"issue":"7407","published-print":{"date-parts":[[2012,7,19]]}},"alternative-id":["BFnature11252"],"URL":"https:\/\/doi.org\/10.1038\/nature11252","relation":{"is-referenced-by":[{"id-type":"doi","id":"10.7554\/eLife.02725","asserted-by":"object"}],"has-review":[{"id-type":"doi","id":"10.3410\/f.717950661.793455968","asserted-by":"object"}]},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,7,18]]},"assertion":[{"value":"15 November 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 May 2012","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 July 2012","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The author declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}