메뉴 건너뛰기




Volumn 6, Issue 3, 2015, Pages 812-840

Epigenetic heterogeneity of B-cell lymphoma: DNA methylation, gene expression and chromatin states

Author keywords

Epigenetic reprogramming; Gene expression; Germinal center; High dimensional data portraying; Machine learning; Promoter methylation; Stemness

Indexed keywords

DNA; MYC PROTEIN; POLYCOMB REPRESSIVE COMPLEX 2; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR EZH2; TRANSCRIPTION FACTOR SUZ12; UNCLASSIFIED DRUG;

EID: 84941210381     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes6030812     Document Type: Article
Times cited : (25)

References (47)
  • 4
    • 33744960411 scopus 로고    scopus 로고
    • A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling
    • Hummel, M.; Bentink, S.; Berger, H.; Klapper, W.; Wessendorf, S.; Barth, T.F.E. A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling. N. Engl. J. Med. 2006, 354, 2419-2430.
    • (2006) N. Engl. J. Med , vol.354 , pp. 2419-2430
    • Hummel, M.1    Bentink, S.2    Berger, H.3    Klapper, W.4    Wessendorf, S.5    Barth, T.F.E.6
  • 5
    • 84901354658 scopus 로고    scopus 로고
    • Portraying the expression landscapes of B-Cell lymphoma-intuitive detection of outlier samples and of molecular subtypes
    • Hopp, L.; Lembcke, K.; Binder, H.; Wirth, H. Portraying the expression landscapes of B-Cell lymphoma-intuitive detection of outlier samples and of molecular subtypes. Biology 2013, 2, 1411-1437.
    • (2013) Biology , vol.2 , pp. 1411-1437
    • Hopp, L.1    Lembcke, K.2    Binder, H.3    Wirth, H.4
  • 8
    • 64049094683 scopus 로고    scopus 로고
    • New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling
    • Martín-Subero, J.I.; Kreuz, M.; Bibikova, M.; Bentink, S.; Ammerpohl, O.; Wickham-Garcia, E.; Siebert, R. New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling. Blood 2009, 113, 2488-2497.
    • (2009) Blood , vol.113 , pp. 2488-2497
    • Martín-Subero, J.I.1    Kreuz, M.2    Bibikova, M.3    Bentink, S.4    Ammerpohl, O.5    Wickham-Garcia, E.6    Siebert, R.7
  • 9
    • 84925281562 scopus 로고    scopus 로고
    • The epigenetic basis of diffuse large B-Cell lymphoma
    • Jiang, Y.; Melnick, A. The epigenetic basis of diffuse large B-Cell lymphoma. Semin. Hematol. 2015, 52, 86-96.
    • (2015) Semin. Hematol , vol.52 , pp. 86-96
    • Jiang, Y.1    Melnick, A.2
  • 10
    • 84923351501 scopus 로고    scopus 로고
    • Polycomb genes, miRNA, and their deregulation in B-cell malignancies
    • Wang, G.G.; Konze, K.D.; Tao, J. Polycomb genes, miRNA, and their deregulation in B-cell malignancies. Blood 2015, 125, 1217-1225.
    • (2015) Blood , vol.125 , pp. 1217-1225
    • Wang, G.G.1    Konze, K.D.2    Tao, J.3
  • 11
    • 84939545459 scopus 로고    scopus 로고
    • (accessed on 20 August 2015)
    • Non-Hodgkin Lymphoma Statistics. Available online: http://www.cancerresearchuk.org/cancerinfo/ cancerstats/types/nhl (accessed on 20 August 2015).
    • Non-Hodgkin Lymphoma Statistics
  • 12
    • 84916217121 scopus 로고    scopus 로고
    • Portraying the expression landscapes of cancer subtypes: A glioblastoma multiforme and prostate cancer case study
    • Hopp, L.; Wirth, H.; Fasold, M.; Binder, H. Portraying the expression landscapes of cancer subtypes: A glioblastoma multiforme and prostate cancer case study. Syst. Biomed. 2013, doi:10.4161/sysb.25897.
    • (2013) Syst. Biomed
    • Hopp, L.1    Wirth, H.2    Fasold, M.3    Binder, H.4
  • 14
    • 84939952838 scopus 로고    scopus 로고
    • Molecular classification of diffuse cerebral WHO grade II/III gliomas using genome-and transcriptome-wide profiling improves stratification of prognostically distinct patient groups
    • Weller, M.; Weber, R.; Willscher, E.; Riehmer, V.; Hentschel, B.; Kreuz, M.; Reifenberger, G.; Felsberg, J.; Beyer, U.; Löffler-Wirth, H.; et al. Molecular classification of diffuse cerebral WHO grade II/III gliomas using genome-and transcriptome-wide profiling improves stratification of prognostically distinct patient groups. Acta Neuropathol. 2015, 129, 679-693.
    • (2015) Acta Neuropathol , vol.129 , pp. 679-693
    • Weller, M.1    Weber, R.2    Willscher, E.3    Riehmer, V.4    Hentschel, B.5    Kreuz, M.6    Reifenberger, G.7    Felsberg, J.8    Beyer, U.9    Löffler-Wirth, H.10
  • 16
    • 79960662814 scopus 로고    scopus 로고
    • Expression cartography of human tissues using self organizing maps
    • Wirth, H.; Loeffler, M.; von Bergen, M.; Binder, H. Expression cartography of human tissues using self organizing maps. BMC Bioinf. 2011, doi:10.1186/1471-2105-12-306.
    • (2011) BMC Bioinf
    • Wirth, H.1    Loeffler, M.2    von Bergen, M.3    Binder, H.4
  • 17
    • 84867095369 scopus 로고    scopus 로고
    • Mining SOM expression portraits: Feature selection and integrating concepts of molecular function
    • Wirth, H.; von Bergen, M.; Binder, H. Mining SOM expression portraits: Feature selection and integrating concepts of molecular function. BioData Min. 2012, doi:10.1186/1756-0381-5-18.
    • (2012) BioData Min
    • Wirth, H.1    von Bergen, M.2    Binder, H.3
  • 18
    • 84943388769 scopus 로고    scopus 로고
    • OposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor
    • Wirth-Loeffler, H.; Kalcher, M.; Binder, H. OposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. Bioinformatics 2015, doi:10.1093/bioinformatics/btv342.
    • (2015) Bioinformatics
    • Wirth-Loeffler, H.1    Kalcher, M.2    Binder, H.3
  • 19
    • 70449392630 scopus 로고    scopus 로고
    • Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
    • Toronen, P.; Ojala, P.; Marttinen, P.; Holm, L. Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. BMC Bioinf. 2009, doi:10.1186/1471-2105-10-307.
    • (2009) BMC Bioinf
    • Toronen, P.1    Ojala, P.2    Marttinen, P.3    Holm, L.4
  • 23
    • 78650821207 scopus 로고    scopus 로고
    • PCL2 modulates gene regulatory networks controlling self-renewal and commitment in embryonic stem cells
    • Walker, E.; Manias, J.L.; Chang, W.Y.; Stanford, W.L. PCL2 modulates gene regulatory networks controlling self-renewal and commitment in embryonic stem cells. Cell Cycle 2011, 10, 45-51.
    • (2011) Cell Cycle , vol.10 , pp. 45-51
    • Walker, E.1    Manias, J.L.2    Chang, W.Y.3    Stanford, W.L.4
  • 24
    • 77952449085 scopus 로고    scopus 로고
    • Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features
    • Ang, P.; Loh, M.; Liem, N.; Lim, P.; Grieu, F.; Vaithilingam, A.; Platell, C.; Yong, W.P.; Iacopetta, B.; Soong, R. Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features. BMC Cancer 2010, doi:10.1186/1471-2407-10-227.
    • (2010) BMC Cancer
    • Ang, P.1    Loh, M.2    Liem, N.3    Lim, P.4    Grieu, F.5    Vaithilingam, A.6    Platell, C.7    Yong, W.P.8    Iacopetta, B.9    Soong, R.10
  • 27
    • 30044451287 scopus 로고    scopus 로고
    • Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification
    • Kim, Y.H.; Girard, L.; Giacomini, C.P.; Wang, P.; Hernandez-Boussard, T.; Tibshirani, R.; Minna, J.D.; Pollack, J.R. Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification. Oncogene 2005, 25, 130-138.
    • (2005) Oncogene , vol.25 , pp. 130-138
    • Kim, Y.H.1    Girard, L.2    Giacomini, C.P.3    Wang, P.4    Hernandez-Boussard, T.5    Tibshirani, R.6    Minna, J.D.7    Pollack, J.R.8
  • 33
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489, 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • The ENCODE Project Consortium.1
  • 35
    • 84884784742 scopus 로고    scopus 로고
    • Age-associated epigenetic drift: Implications, and a case of epigenetic thrift? Hum
    • Teschendorff, A.E.; West, J.; Beck, S. Age-associated epigenetic drift: implications, and a case of epigenetic thrift? Hum. Mol. Genet. 2013, 22, R7-R15.
    • (2013) Mol. Genet , vol.22 , pp. R7-R15
    • Teschendorff, A.E.1    West, J.2    Beck, S.3
  • 38
    • 0347624593 scopus 로고    scopus 로고
    • Role for BRG1 in cell cycle control and tumor suppression
    • Hendricks, K.B.; Shanahan, F.; Lees, E. Role for BRG1 in cell cycle control and tumor suppression. Mol. Cell. Biol. 2004, 24, 362-376.
    • (2004) Mol. Cell. Biol , vol.24 , pp. 362-376
    • Hendricks, K.B.1    Shanahan, F.2    Lees, E.3
  • 39
    • 78650062951 scopus 로고    scopus 로고
    • EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis
    • Velichutina, I.; Shaknovich, R.; Geng, H.; Johnson, N.A.; Gascoyne, R.D.; Melnick, A.M.; Elemento, O. EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood 2010, 116, 5247-5255.
    • (2010) Blood , vol.116 , pp. 5247-5255
    • Velichutina, I.1    Shaknovich, R.2    Geng, H.3    Johnson, N.A.4    Gascoyne, R.D.5    Melnick, A.M.6    Elemento, O.7
  • 41
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst, J.; Kellis, M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotech. 2010, 28, 817-825.
    • (2010) Nat. Biotech , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 44
    • 84866320759 scopus 로고    scopus 로고
    • Identification of human germinal center light and dark zone cells and their relationship to human B-cell lymphomas
    • Victora, G.D.; Dominguez-Sola, D.; Holmes, A.B.; Deroubaix, S.; Dalla-Favera, R.; Nussenzweig, M.C. Identification of human germinal center light and dark zone cells and their relationship to human B-cell lymphomas. Blood 2012, 120, 2240-2248.
    • (2012) Blood , vol.120 , pp. 2240-2248
    • Victora, G.D.1    Dominguez-Sola, D.2    Holmes, A.B.3    Deroubaix, S.4    Dalla-Favera, R.5    Nussenzweig, M.C.6
  • 46
    • 84923813876 scopus 로고    scopus 로고
    • Dynamics of B cells in germinal centres
    • De Silva, N.S.; Klein, U. Dynamics of B cells in germinal centres. Nat. Rev. Immunol. 2015, 15, 137-148.
    • (2015) Nat. Rev. Immunol , vol.15 , pp. 137-148
    • De Silva, N.S.1    Klein, U.2
  • 47
    • 84879260661 scopus 로고    scopus 로고
    • A double take on bivalent promoters
    • Voigt, P.; Tee, W.-W.; Reinberg, D. A double take on bivalent promoters. Genes Dev. 2013, 27, 1318-1338.
    • (2013) Genes Dev , vol.27 , pp. 1318-1338
    • Voigt, P.1    Tee, W.-W.2    Reinberg, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.