TY - JOUR AU - Perou, C. M. AU - Sorlie, T. AU - Eisen, M. B. AU - Rijn, M. AU - Jeffrey, S. S. AU - Rees, C. A. AU - Pollack, J. R. AU - Ross, D. T. AU - Johnsen, H. AU - Akslen, L. A. PY - 2000 DA - 2000// TI - Molecular portraits of human breast tumours JO - Nature VL - 406 UR - https://doi.org/10.1038/35021093 DO - 10.1038/35021093 ID - Perou2000 ER - TY - JOUR AU - Alizadeh, A. AU - Eisen, M. AU - Davis, R. E. AU - Ma, C. AU - Sabet, H. AU - Tran, T. AU - Powell, J. I. AU - Yang, L. AU - Marti, G. E. AU - Moore, D. T. PY - 1999 DA - 1999// TI - The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes JO - Cold Spring Harb Symp Quant Biol VL - 64 UR - https://doi.org/10.1101/sqb.1999.64.71 DO - 10.1101/sqb.1999.64.71 ID - Alizadeh1999 ER - TY - JOUR AU - Pollack, J. R. AU - Perou, C. M. AU - Alizadeh, A. A. AU - Eisen, M. B. AU - Pergamenschikov, A. AU - Williams, C. F. AU - Jeffrey, S. S. AU - Botstein, D. AU - Brown, P. O. PY - 1999 DA - 1999// TI - Genome-wide analysis of DNA copy-number changes using cDNA microarrays JO - Nat Genet VL - 23 UR - https://doi.org/10.1038/14385 DO - 10.1038/14385 ID - Pollack1999 ER - TY - JOUR AU - Tusher, V. G. AU - Tibshirani, R. AU - Chu, G. PY - 2001 DA - 2001// TI - Significance analysis of microarrays applied to the ionizing radiation response JO - Proc Natl Acad Sci U S A VL - 98 UR - https://doi.org/10.1073/pnas.091062498 DO - 10.1073/pnas.091062498 ID - Tusher2001 ER - TY - JOUR AU - Smyth, G. K. PY - 2004 DA - 2004// TI - Linear models and empirical bayes methods for assessing differential expression in microarray experiments JO - Stat Appl Genet Mol Biol VL - 3 ID - Smyth2004 ER - TY - JOUR AU - Wettenhall, J. M. AU - Smyth, G. K. PY - 2004 DA - 2004// TI - limmaGUI: a graphical user interface for linear modeling of microarray data JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth449 DO - 10.1093/bioinformatics/bth449 ID - Wettenhall2004 ER - TY - JOUR AU - Wilcoxon, F. PY - 1945 DA - 1945// TI - Individual comparisons by ranking methods JO - Biom Bull VL - 1 UR - https://doi.org/10.2307/3001968 DO - 10.2307/3001968 ID - Wilcoxon1945 ER - TY - STD TI - Feinberg AP. Epigenetic stochasticity, nuclear structure and cancer: the implications for medicine. J Intern Med. 2014;276(1):5-11. ID - ref8 ER - TY - JOUR AU - Feinberg, A. P. AU - Irizarry, R. A. PY - 2010 DA - 2010// TI - Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.0906183107 DO - 10.1073/pnas.0906183107 ID - Feinberg2010 ER - TY - JOUR AU - Hansen, K. D. AU - Timp, W. AU - Bravo, H. C. AU - Sabunciyan, S. AU - Langmead, B. AU - McDonald, O. G. AU - Wen, B. AU - Wu, H. AU - Liu, Y. AU - Diep, D. PY - 2011 DA - 2011// TI - Increased methylation variation in epigenetic domains across cancer types JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.865 DO - 10.1038/ng.865 ID - Hansen2011 ER - TY - JOUR AU - Feinberg, A. P. AU - Ohlsson, R. AU - Henikoff, S. PY - 2006 DA - 2006// TI - The epigenetic progenitor origin of human cancer JO - Nat Rev Genet VL - 7 UR - https://doi.org/10.1038/nrg1748 DO - 10.1038/nrg1748 ID - Feinberg2006 ER - TY - JOUR AU - Issa, J. P. PY - 2011 DA - 2011// TI - Epigenetic variation and cellular Darwinism JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.897 DO - 10.1038/ng.897 ID - Issa2011 ER - TY - JOUR AU - Teschendorff, A. E. AU - Jones, A. AU - Fiegl, H. AU - Sargent, A. AU - Zhuang, J. J. AU - Kitchener, H. C. AU - Widschwendter, M. PY - 2012 DA - 2012// TI - Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation JO - Genome Med VL - 4 UR - https://doi.org/10.1186/gm323 DO - 10.1186/gm323 ID - Teschendorff2012 ER - TY - JOUR AU - Teschendorff, A. E. AU - Widschwendter, M. PY - 2012 DA - 2012// TI - Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts170 DO - 10.1093/bioinformatics/bts170 ID - Teschendorff2012 ER - TY - JOUR AU - Teschendorff, A. E. AU - Liu, X. AU - Caren, H. AU - Pollard, S. M. AU - Beck, S. AU - Widschwendter, M. AU - Chen, L. PY - 2014 DA - 2014// TI - The dynamics of DNA methylation covariation patterns in carcinogenesis JO - PLoS Comput Biol VL - 10 UR - https://doi.org/10.1371/journal.pcbi.1003709 DO - 10.1371/journal.pcbi.1003709 ID - Teschendorff2014 ER - TY - JOUR AU - Shibata, D. PY - 2006 DA - 2006// TI - Clonal diversity in tumor progression JO - Nat Genet VL - 38 UR - https://doi.org/10.1038/ng0406-402 DO - 10.1038/ng0406-402 ID - Shibata2006 ER - TY - JOUR AU - Bernstein, C. AU - Nfonsam, V. AU - Prasad, A. R. AU - Bernstein, H. PY - 2013 DA - 2013// TI - Epigenetic field defects in progression to cancer JO - World J Gastrointest Oncol VL - 5 UR - https://doi.org/10.4251/wjgo.v5.i3.43 DO - 10.4251/wjgo.v5.i3.43 ID - Bernstein2013 ER - TY - JOUR AU - Katsurano, M. AU - Niwa, T. AU - Yasui, Y. AU - Shigematsu, Y. AU - Yamashita, S. AU - Takeshima, H. AU - Lee, M. S. AU - Kim, Y. J. AU - Tanaka, T. AU - Ushijima, T. PY - 2012 DA - 2012// TI - Early-stage formation of an epigenetic field defect in a mouse colitis model, and non-essential roles of T- and B-cells in DNA methylation induction JO - Oncogene VL - 31 UR - https://doi.org/10.1038/onc.2011.241 DO - 10.1038/onc.2011.241 ID - Katsurano2012 ER - TY - JOUR AU - Phipson, B. AU - Oshlack, A. PY - 2014 DA - 2014// TI - DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0465-4 DO - 10.1186/s13059-014-0465-4 ID - Phipson2014 ER - TY - STD TI - Ahn S, Wang T. A powerful statistical method for identifying differentially methylated markers in complex diseases. Pac Symp Biocomput. 2013;69–79. ID - ref20 ER - TY - JOUR AU - Wahl, S. AU - Fenske, N. AU - Zeilinger, S. AU - Suhre, K. AU - Gieger, C. AU - Waldenberger, M. AU - Grallert, H. AU - Schmid, M. PY - 2014 DA - 2014// TI - On the potential of models for location and scale for genome-wide DNA methylation data JO - BMC Bioinformatics VL - 15 UR - https://doi.org/10.1186/1471-2105-15-232 DO - 10.1186/1471-2105-15-232 ID - Wahl2014 ER - TY - JOUR AU - Teschendorff, A. E. AU - Gao, Y. AU - Jones, A. AU - Ruebner, M. AU - Beckmann, M. W. AU - Wachter, D. L. AU - Fasching, P. A. AU - Widschwendter, M. PY - 2016 DA - 2016// TI - DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms10478 DO - 10.1038/ncomms10478 ID - Teschendorff2016 ER - TY - JOUR AU - Aryee, M. J. AU - Jaffe, A. E. AU - Corrada-Bravo, H. AU - Ladd-Acosta, C. AU - Feinberg, A. P. AU - Hansen, K. D. AU - Irizarry, R. A. PY - 2014 DA - 2014// TI - Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu049 DO - 10.1093/bioinformatics/btu049 ID - Aryee2014 ER - TY - JOUR AU - Teschendorff, A. E. AU - Marabita, F. AU - Lechner, M. AU - Bartlett, T. AU - Tegner, J. AU - Gomez-Cabrero, D. AU - Beck, S. PY - 2013 DA - 2013// TI - A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts680 DO - 10.1093/bioinformatics/bts680 ID - Teschendorff2013 ER - TY - BOOK AU - Snedecor, G. W. AU - Cochran, W. G. PY - 1989 DA - 1989// TI - Statistical methods ID - Snedecor1989 ER - TY - STD TI - Xu X, Su S, Barnes VA, De Miguel C, Pollock J, Ownby D, Shi H, Zhu H, Snieder H, Wang X. A genome-wide methylation study on obesity: Differential variability and differential methylation. Epigenetics. 2013;8(5):522-33. ID - ref26 ER - TY - JOUR AU - Storey, J. D. AU - Tibshirani, R. PY - 2003 DA - 2003// TI - Statistical significance for genomewide studies JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.1530509100 DO - 10.1073/pnas.1530509100 ID - Storey2003 ER - TY - JOUR AU - Teschendorff, A. E. AU - Menon, U. AU - Gentry-Maharaj, A. AU - Ramus, S. J. AU - Gayther, S. A. AU - Apostolidou, S. AU - Jones, A. AU - Lechner, M. AU - Beck, S. AU - Jacobs, I. J. AU - Widschwendter, M. PY - 2009 DA - 2009// TI - An epigenetic signature in peripheral blood predicts active ovarian cancer JO - PLoS One VL - 4 UR - https://doi.org/10.1371/journal.pone.0008274 DO - 10.1371/journal.pone.0008274 ID - Teschendorff2009 ER - TY - JOUR AU - Dedeurwaerder, S. AU - Desmedt, C. AU - Calonne, E. AU - Singhal, S. K. AU - Haibe-Kains, B. AU - Defrance, M. AU - Michiels, S. AU - Volkmar, M. AU - Deplus, R. AU - Luciani, J. PY - 2011 DA - 2011// TI - DNA methylation profiling reveals a predominant immune component in breast cancers JO - EMBO Mol Med VL - 3 UR - https://doi.org/10.1002/emmm.201100801 DO - 10.1002/emmm.201100801 ID - Dedeurwaerder2011 ER - TY - JOUR AU - Teschendorff, A. E. AU - Miremadi, A. AU - Pinder, S. E. AU - Ellis, I. O. AU - Caldas, C. PY - 2007 DA - 2007// TI - An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-8-r157 DO - 10.1186/gb-2007-8-8-r157 ID - Teschendorff2007 ER - TY - JOUR AU - Subramanian, A. AU - Tamayo, P. AU - Mootha, V. K. AU - Mukherjee, S. AU - Ebert, B. L. AU - Gillette, M. A. AU - Paulovich, A. AU - Pomeroy, S. L. AU - Golub, T. R. AU - Lander, E. S. AU - Mesirov, J. P. PY - 2005 DA - 2005// TI - Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0506580102 DO - 10.1073/pnas.0506580102 ID - Subramanian2005 ER - TY - JOUR AU - Yuan, T. AU - Jiao, Y. AU - Jong, S. AU - Ophoff, R. A. AU - Beck, S. AU - Teschendorff, A. E. PY - 2015 DA - 2015// TI - An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1004996 DO - 10.1371/journal.pgen.1004996 ID - Yuan2015 ER - TY - JOUR AU - Chen, Y. A. AU - Lemire, M. AU - Choufani, S. AU - Butcher, D. T. AU - Grafodatskaya, D. AU - Zanke, B. W. AU - Gallinger, S. AU - Hudson, T. J. AU - Weksberg, R. PY - 2013 DA - 2013// TI - Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray JO - Epigenetics VL - 8 UR - https://doi.org/10.4161/epi.23470 DO - 10.4161/epi.23470 ID - Chen2013 ER - TY - JOUR AU - Teschendorff, A. E. AU - Zhuang, J. AU - Widschwendter, M. PY - 2011 DA - 2011// TI - Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr171 DO - 10.1093/bioinformatics/btr171 ID - Teschendorff2011 ER - TY - JOUR AU - Wang, N. AU - Hoffman, E. P. AU - Chen, L. AU - Chen, L. AU - Zhang, Z. AU - Liu, C. AU - Yu, G. AU - Herrington, D. M. AU - Clarke, R. AU - Wang, Y. PY - 2016 DA - 2016// TI - Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep18909 DO - 10.1038/srep18909 ID - Wang2016 ER - TY - JOUR AU - Santagata, S. AU - Thakkar, A. AU - Ergonul, A. AU - Wang, B. AU - Woo, T. AU - Hu, R. AU - Harrell, J. C. AU - McNamara, G. AU - Schwede, M. AU - Culhane, A. C. PY - 2014 DA - 2014// TI - Taxonomy of breast cancer based on normal cell phenotype predicts outcome JO - J Clin Invest VL - 124 UR - https://doi.org/10.1172/JCI70941 DO - 10.1172/JCI70941 ID - Santagata2014 ER - TY - JOUR AU - Santagata, S. AU - Ince, T. A. PY - 2014 DA - 2014// TI - Normal cell phenotypes of breast epithelial cells provide the foundation of a breast cancer taxonomy JO - Expert Rev Anticancer Ther VL - 14 UR - https://doi.org/10.1586/14737140.2014.956096 DO - 10.1586/14737140.2014.956096 ID - Santagata2014 ER - TY - JOUR AU - Rakyan, V. K. AU - Down, T. A. AU - Balding, D. J. AU - Beck, S. PY - 2011 DA - 2011// TI - Epigenome-wide association studies for common human diseases JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg3000 DO - 10.1038/nrg3000 ID - Rakyan2011 ER -