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Autor:
Gary S. Stein, Terri L. Messier, Job Dekker, Deli Hong, Jane B. Lian, Andre J. van Wijnen, Bryan R. Lajoie, A. Rasim Barutcu, Anthony N. Imbalzano, Rachel Patton McCord, Coralee E. Tye, Gillian Browne, Janet L. Stein
Publikováno v:
Genome Biology
Background Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin
Autor:
Steve Horvath
Publikováno v:
Genome Biology
I recently described an epigenetic biomarker of aging based on DNA methylation (DNAm) levels [1]. Unfortunately, I made a software coding error in my analysis of the cancer data, but not of the non-cancer tissue data. The error effectively added an o
Autor:
Zhen Ye, Celso A. Espinoza, Alexander V. Strunnikov, Susan Robinson, Sungyun Kang, Teruhiko Suzuki, Samuel Rivero-Hinojosa, Vijayaraj Nagarajan, Claudia Fabiola Méndez-Catalá, John E.J. Rasko, Dmitri Loukinov, Victor V. Lobanenkov, Bing Ren, Abdelhalim Boukaba, Elena M. Pugacheva, Natsuki Kosaka-Suzuki
Publikováno v:
Genome biology, vol 16, iss 1
Genome Biology
Genome Biology
Background CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation. Results Here we show that these t
Autor:
Rafal T. Marszalek
Publikováno v:
Genome Biology
It was one Saturday morning in April when, after a 24-hour journey across half of the world, and a very early morning start to the 2014 AACR annual meeting marathon, I was sitting in a dark room in the San Diego Convention Center listening to Korneli
Autor:
Grace O. Silva, Joel S. Parker, Mengjie Chen, Charles M. Perou, Wei Sun, Lisle E. Mose, Marni B. Siegel
Publikováno v:
Genome Biology
Genome Biology, Vol 18, Iss 1, Pp 1-14 (2017)
Genome Biology, Vol 18, Iss 1, Pp 1-14 (2017)
Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues limit current CNA calling based upon DNA
Autor:
Samuel Aparicio, Christina Curtis, Suet-Feung Chin, Oscar M. Rueda, H. Raza Ali, Carlos Caldas, Mark J Dunning
Publikováno v:
Genome Biology
Background IntClust is a classification of breast cancer comprising 10 subtypes based on molecular drivers identified through the integration of genomic and transcriptomic data from 1,000 breast tumors and validated in a further 1,000. We present a r
Autor:
Juan P. Palazzo, John Quackenbush, Karen E. Rasmussen, Yuzhi Yin, Subhashini Chandrasekharan, Levy Kopelovich, Zhiyuan Hu, Gary A. Churchill, Andrey Khramtsov, Jeffrey E. Green, Charles M. Perou, Jason I. Herschkowitz, Olufunmilayo I. Olopade, Laundette P. Jones, Powel H. Brown, Victor J. Weigman, Igor Mikaelian, Michael G. Backlund, Philip S. Bernard, Priscilla A. Furth, Roy Bastein, Robert I. Glazer, Karl Simin, Jerry Usary, Terry Van Dyke, Shahin Assefnia
Publikováno v:
Genome biology, vol 8, iss 5
Genome Biology
Genome Biology
Comparison of mammary tumor gene-expression profiles from thirteen murine models using microarrays and with that of human breast tumors showed that many of the defining characteristics of human subtypes were conserved among mouse models.
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Autor:
Carlos Caldas, Nuno L. Barbosa-Morais, Andrew R. Green, Simon Tavaré, Peggy L. Porter, Bauke Ylstra, Natalie P. Thorne, Ian O. Ellis, Andrew E. Teschendorff, James D. Brenton, Yanzhong Wang, John C. Marioni, Sarah E Pinder, José Luis Costa, Mark A. van de Wiel, S.F. Chin
Publikováno v:
Chin, S F, Teschendorff, A E, Marioni, J C, Wang, Y, Barbosa-Morais, N L, Thorne, N P, Costa, J L, Pinder, S E, Van de Wiel, M A, Green, A R, Ellis, I O, Porter, P L, Tavaré, S, Brenton, J D, Ylstra, B & Caldas, C 2007, ' High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer ', Genome Biology, vol. 8, no. 10, R215 . https://doi.org/10.1186/gb-2007-8-10-r215
Genome Biology, 8. Springer Verlag
Genome Biology
Genome Biology, 8(10):R215. BioMed Central Ltd.
Chin, S F, Teschendorff, A E, Marioni, J C, Wang, Y, Barbosa-Morais, N L, Thorne, N P, Costa, J L, Pinder, S E, van de Wiel, M A, Green, A, Ellis, I O, Porter, P L, Tavaré, S, Brenton, J D, Ylstra, B & Caldas, C 2007, ' High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer ', Genome Biology, vol. 8, pp. R215 . https://doi.org/10.1186/gb-2007-8-10-r215
Genome Biology, 8. Springer Verlag
Genome Biology
Genome Biology, 8(10):R215. BioMed Central Ltd.
Chin, S F, Teschendorff, A E, Marioni, J C, Wang, Y, Barbosa-Morais, N L, Thorne, N P, Costa, J L, Pinder, S E, van de Wiel, M A, Green, A, Ellis, I O, Porter, P L, Tavaré, S, Brenton, J D, Ylstra, B & Caldas, C 2007, ' High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer ', Genome Biology, vol. 8, pp. R215 . https://doi.org/10.1186/gb-2007-8-10-r215
High resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer, and provides a genome-wide list of common copy number alterations associated with aberrant expression and poor prognosis.
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Backgro
Autor:
Christine Desmedt, Christos Sotiriou, Benjamin Haibe-Kains, Martine Piccart, Gianluca Bontempi, Françoise Rothé
Publikováno v:
Genome biology, 11 (2
Genome Biology
Genome Biology
Early gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative
Autor:
Alayne L. Brunner, Robert T. Sweeney, Sushama Varma, Jun Li, Robert Tibshirani, Rui Li, Robert B. West, Shirley Zhu, Xiangqian Guo
Publikováno v:
Genome Biology
Background: The earliest recognizable stages of breast neoplasia are lesions that represent a heterogeneous collection of epithelial proliferations currently classified based on morphology. Their role in the development of breast cancer is not well u