{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:10:52Z","timestamp":1772165452162,"version":"3.50.1"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,5,25]],"date-time":"2018-05-25T00:00:00Z","timestamp":1527206400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"crossref","award":["EP\/J500240\/1"],"award-info":[{"award-number":["EP\/J500240\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2204-4","type":"journal-article","created":{"date-parts":[[2018,5,25]],"date-time":"2018-05-25T07:13:08Z","timestamp":1527232388000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["polyClustR: defining communities of reconciled cancer subtypes with biological and prognostic significance"],"prefix":"10.1186","volume":"19","author":[{"given":"Katherine","family":"Eason","sequence":"first","affiliation":[]},{"given":"Gift","family":"Nyamundanda","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8485-5150","authenticated-orcid":false,"given":"Anguraj","family":"Sadanandam","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,5,25]]},"reference":[{"key":"2204_CR1","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1056\/NEJMra043186","volume":"357","author":"CA Hudis","year":"2007","unstructured":"Hudis CA. Trastuzumab \u2014 mechanism of action and use in clinical practice. New Engl J Med. 2007;357:39\u201351.","journal-title":"New Engl J Med"},{"key":"2204_CR2","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1038\/nm.3175","volume":"19","author":"A Sadanandam","year":"2013","unstructured":"Sadanandam A, Lyssiotis CA, Homicsko K, Collisson EA, Gibb WJ, Wullschleger S, Ostos LCG, Lannon WA, Grotzinger C, Del Rio M, et al. A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med. 2013;19:619\u201325.","journal-title":"Nat Med"},{"key":"2204_CR3","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1001\/jamaoncol.2016.2314","volume":"2","author":"N Song","year":"2016","unstructured":"Song N, Pogue-Geile KL, Gavin PG, Yothers G, Rim Kim S, Johnson NL, Lipchick C, Allegra CJ, Petrelli NJ, O'Connell MJ, et al. Clinical outcome from oxaliplatin treatment in stage II\/III colon cancer according to intrinsic subtypes: secondary analysis of NASBP C-07\/NRG oncology randomized clinical trial. JAMA Oncol. 2016;2:1162\u20139.","journal-title":"JAMA Oncol"},{"key":"2204_CR4","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1038\/nm.2344","volume":"17","author":"EA Collisson","year":"2011","unstructured":"Collisson EA, Sadanandam A, Olson P, Gibb WJ, Truitt M, Gu S, Cooc J, Weinkle J, Kim GE, Jakkula L. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med. 2011;17:500\u20133.","journal-title":"Nat Med"},{"key":"2204_CR5","doi-asserted-by":"publisher","first-page":"1168","DOI":"10.1038\/ng.3398","volume":"47","author":"RA Moffitt","year":"2015","unstructured":"Moffitt RA, Marayati R, Flate EL, Volmar KE, Loeza SGH, Hoadley KA, Rashid NU, Williams LA, Eaton SC, Chung AH, et al. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nat Genet. 2015;47:1168\u201378.","journal-title":"Nat Genet"},{"key":"2204_CR6","doi-asserted-by":"publisher","first-page":"2724","DOI":"10.1073\/pnas.1018854108","volume":"109","author":"LM Heiser","year":"2012","unstructured":"Heiser LM, Sadanandam A, Kuo W-L, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci. 2012;109:2724\u20139.","journal-title":"Proc Natl Acad Sci"},{"key":"2204_CR7","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1038\/35021093","volume":"406","author":"CM Perou","year":"2000","unstructured":"Perou CM, S\u00f8rlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, et al. Molecular portraits of human breast tumours. Nature. 2000;406:747\u201352.","journal-title":"Nature"},{"key":"2204_CR8","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.2217\/bmm.15.96","volume":"9","author":"L Wu","year":"2015","unstructured":"Wu L, Liu Z, Xu J, Chen M, Fang H, Tong W, Xiao W. NETBAGs: a network-based clustering approach with gene signatures for cancer subtyping analysis. Biomark Med. 2015;9:1053\u201365.","journal-title":"Biomark Med"},{"key":"2204_CR9","unstructured":"Han J, Pei J, Kamber M. Data mining: concepts and techniques. 3rd ed. USA: Elsevier; 2011."},{"key":"2204_CR10","doi-asserted-by":"publisher","first-page":"353","DOI":"10.4161\/cc.27769","volume":"13","author":"A Sadanandam","year":"2014","unstructured":"Sadanandam A, Wang X, de Sousa EMF, Gray JW, Vermeulen L, Hanahan D, Medema JP. Reconciliation of classification systems defining molecular subtypes of colorectal cancer: interrelationships and clinical implications. Cell Cycle. 2014;13:353\u20137.","journal-title":"Cell Cycle"},{"key":"2204_CR11","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1038\/nm.3967","volume":"21","author":"J Guinney","year":"2015","unstructured":"Guinney J, Dienstmann R, Wang X, de Reyni\u00e8s A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, et al. The consensus molecular subtypes of colorectal cancer. Nat Med. 2015;21:1350\u20136.","journal-title":"Nat Med"},{"key":"2204_CR12","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1086\/304888","volume":"490","author":"JF Navarro","year":"1997","unstructured":"Navarro JF, Frenk CS, White SDM. A universal density profile from hierarchical clustering. Astrophys J. 1997;490:493.","journal-title":"Astrophys J"},{"key":"2204_CR13","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1093\/comjnl\/20.4.364","volume":"20","author":"D Defays","year":"1977","unstructured":"Defays D. An efficient algorithm for a complete link method. Comput J. 1977;20:364\u20136.","journal-title":"Comput J"},{"key":"2204_CR14","first-page":"281","volume":"1","author":"J MacQueen","year":"1967","unstructured":"MacQueen J. Some methods for classification and analysis of multivariate observations. Proceedings of the fifth Berkeley symposium on mathematical statistics and probability. 1967;1:281\u201397.","journal-title":"Proceedings of the fifth Berkeley symposium on mathematical statistics and probability"},{"key":"2204_CR15","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/44565","volume":"401","author":"DD Lee","year":"1999","unstructured":"Lee DD, Seung HS. Learning the parts of objects by non-negative matrix factorization. Nature. 1999;401:788\u201391.","journal-title":"Nature"},{"key":"2204_CR16","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1038\/nm.3174","volume":"19","author":"E De Sousa","year":"2013","unstructured":"De Sousa E, Melo F, Wang X, Jansen M, Fessler E, Trinh A, de Rooij LPMH, de Jong JH, de Boer OJ, van Leersum R, Bijlsma MF, et al. Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions. Nat Med. 2013;19:614\u20138.","journal-title":"Nat Med"},{"key":"2204_CR17","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1002\/path.4212","volume":"231","author":"E Budinska","year":"2013","unstructured":"Budinska E, Popovici V, Tejpar S, D'Ario G, Lapique N, Sikora KO, Di Narzo AF, Yan P, Graeme Hodgson J, Weinrich S, et al. Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer. J Pathol. 2013;231:63\u201376.","journal-title":"J Pathol"},{"key":"2204_CR18","doi-asserted-by":"publisher","first-page":"e1001453","DOI":"10.1371\/journal.pmed.1001453","volume":"10","author":"L Marisa","year":"2013","unstructured":"Marisa L, de Reyni\u00e8s A, Duval A, Selves J, Gaub MP, Vescovo L, Etienne-Grimaldi MC, Schiappa R, Guenot D, Ayadi M, et al. Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS Med. 2013;10:e1001453.","journal-title":"PLoS Med"},{"key":"2204_CR19","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1002\/ijc.28387","volume":"134","author":"P Roepman","year":"2013","unstructured":"Roepman P, Schlicker A, Tabernero J, Majewski I, Tian S, Moreno V, Snel MH, Chresta CM, Rosenberg R, Nitsche U, et al. Colorectal cancer intrinsic subtypes predict chemotherapy benefit, deficient mismatch repair and epithelial-to-mesenchymal transition. Int J Cancer. 2013;134:552\u201362.","journal-title":"Int J Cancer"},{"key":"2204_CR20","first-page":"1","volume":"5","author":"A Schlicker","year":"2012","unstructured":"Schlicker A, Beran G, Chresta CM, McWalter G, Pritchard A, Weston S, Runswick S, Davenport S, Heathcote K, Castro DA, et al. Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines. BMC Med Genet. 2012;5:1\u201315.","journal-title":"BMC Med Genet"},{"key":"2204_CR21","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1016\/j.ccr.2006.10.009","volume":"10","author":"K Chin","year":"2006","unstructured":"Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006;10:529\u201341.","journal-title":"Cancer Cell"},{"key":"2204_CR22","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1158\/0008-5472.CAN-10-0605","volume":"71","author":"C Laurent","year":"2011","unstructured":"Laurent C, Valet F, Planque N, Silveri L, Maacha S, Anezo O, Hupe P, Plancher C, Reyes C, Albaud B, et al. High PTP4A3 phosphatase expression correlates with metastatic risk in uveal melanoma patients. Cancer Res. 2011;71:666\u201374.","journal-title":"Cancer Res"},{"key":"2204_CR23","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1186\/s13148-016-0243-0","volume":"8","author":"PL Triozzi","year":"2016","unstructured":"Triozzi PL, Achberger S, Aldrich W, Crabb JW, Saunthararajah Y, Singh AD. Association of tumor and plasma microRNA expression with tumor monosomy-3 in patients with uveal melanoma. Clin Epigenetics. 2016;8:80.","journal-title":"Clin Epigenetics"},{"issue":"5","key":"2204_CR24","doi-asserted-by":"publisher","first-page":"1234","DOI":"10.1158\/1078-0432.CCR-15-2071","volume":"22","author":"MG Field","year":"2016","unstructured":"Field MG, Decatur CL, Kurtenbach S, Gezgin G, van der Velden PA, Jager MJ, Kozak KN, Harbour JW. PRAME as an independent biomarker for metastasis in uveal melanoma. Clin Cancer Res. 2016;22(5):1234\u201342.","journal-title":"Clin Cancer Res"},{"key":"2204_CR25","doi-asserted-by":"publisher","first-page":"33","DOI":"10.2307\/1217208","volume":"11","author":"RR Sokal","year":"1962","unstructured":"Sokal RR, Rohlf FJ. The comparison of Dendrograms by objective methods. Taxon. 1962;11:33\u201340.","journal-title":"Taxon"},{"key":"2204_CR26","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","volume":"20","author":"PJ Rousseeuw","year":"1987","unstructured":"Rousseeuw PJ. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math. 1987;20:53\u201365.","journal-title":"J Comput Appl Math"},{"key":"2204_CR27","doi-asserted-by":"publisher","first-page":"36106","DOI":"10.1103\/PhysRevE.76.036106","volume":"76","author":"UN Raghavan","year":"2007","unstructured":"Raghavan UN, Albert R, Kumara S. Near linear time algorithm to detect community structures in large-scale networks. Phys Rev E. 2007;76:36106.","journal-title":"Phys Rev E"},{"key":"2204_CR28","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102:15545\u201350.","journal-title":"Proc Natl Acad Sci"},{"key":"2204_CR29","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1093\/bioinformatics\/btq170","volume":"26","author":"MD Wilkerson","year":"2010","unstructured":"Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26:1572\u20133.","journal-title":"Bioinformatics"},{"key":"2204_CR30","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1186\/1471-2105-11-367","volume":"11","author":"R Gaujoux","year":"2010","unstructured":"Gaujoux R, Seoighe C. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics. 2010;11:367.","journal-title":"BMC Bioinformatics"},{"key":"2204_CR31","first-page":"1","volume":"2006","author":"G Cs\u00e1rdi","year":"1695","unstructured":"Cs\u00e1rdi G, Nepusz T. The igraph software package for complex network research. InterJournal Complex Systems. 1695;2006:1\u20139.","journal-title":"InterJournal Complex Systems"},{"key":"2204_CR32","volume-title":"R package version 2.0.4","author":"M Maechler","year":"2016","unstructured":"Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K. Cluster: cluster analysis basics and extensions. In: R package version 2.0.4; 2016."},{"key":"2204_CR33","volume-title":"R package version 2.37\u20134","author":"T Therneau","year":"2014","unstructured":"Therneau T. A package for survival analysis in S. In: R package version 2.37\u20134; 2014."},{"issue":"14","key":"2204_CR34","doi-asserted-by":"publisher","first-page":"8418","DOI":"10.1073\/pnas.0932692100","volume":"100","author":"T Sorlie","year":"2003","unstructured":"Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A. 2003;100(14):8418\u201323.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2204_CR35","doi-asserted-by":"crossref","unstructured":"Onken MD, La W, Ehlers JP, Harbour JW. Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death advances in brief gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res. 2004;64(20):7205\u20139.","DOI":"10.1158\/0008-5472.CAN-04-1750"},{"key":"2204_CR36","doi-asserted-by":"publisher","first-page":"567","DOI":"10.2353\/jmoldx.2006.060077","volume":"8","author":"MD Onken","year":"2006","unstructured":"Onken MD, Worley LA, D\u00e1vila RM, Char DH, Harbour JW. Prognostic testing in uveal melanoma by transcriptomic profiling of fine needle biopsy specimens. J Mol Diagn. 2006;8:567\u201373.","journal-title":"J Mol Diagn"},{"key":"2204_CR37","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1158\/1078-0432.CCR-06-2401","volume":"13","author":"LA Worley","year":"2007","unstructured":"Worley LA, Onken MD, Person E, Robirds D, Branson J, Char DH, Perry A, Harbour JW. Transcriptomic versus chromosomal prognostic markers and clinical outcome in uveal melanoma. Clin Cancer Res. 2007;13:1466\u201371.","journal-title":"Clin Cancer Res"},{"key":"2204_CR38","doi-asserted-by":"publisher","first-page":"6567","DOI":"10.1073\/pnas.082099299","volume":"99","author":"R Tibshirani","year":"2002","unstructured":"Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci. 2002;99:6567\u201372.","journal-title":"Proc Natl Acad Sci"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2204-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2204-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2204-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,24]],"date-time":"2019-05-24T19:04:17Z","timestamp":1558724657000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2204-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5,25]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2204"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2204-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/228551","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,5,25]]},"assertion":[{"value":"10 December 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 May 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 May 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"AS has ownership interest as a patent inventor for a patent entitled \u201cColorectal cancer classification with different prognosis and personalized therapeutic responses\u201d (patent number PCT\/IB2013\/060416). No potential conflicts of interest were disclosed by the other authors.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"182"}}