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Volumn 29, Issue 1, 2013, Pages 22-28

A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC HORMONE AGONISTS AND ANTAGONISTS; ESTROGEN RECEPTOR ALPHA; ESTROGEN RECEPTOR ALPHA, HUMAN; TAMOXIFEN;

EID: 84871756139     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts639     Document Type: Article
Times cited : (8)

References (30)
  • 1
    • 0000353178 scopus 로고
    • A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains
    • Baum, L.E. et al. (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Stat., 41, 164-171.
    • (1970) Ann. Math. Stat. , vol.41 , pp. 164-171
    • Baum, L.E.1
  • 2
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 0032537396 scopus 로고    scopus 로고
    • Tamoxifen for early breast cancer: An overview of the randomised trials
    • Early Breast Cancer Trialists' Collaborative Group (EBCTCG).
    • Early Breast Cancer Trialists' Collaborative Group (EBCTCG). (1998) Tamoxifen for early breast cancer: an overview of the randomised trials. Lancet, 351, 1451-1467.
    • (1998) Lancet , vol.351 , pp. 1451-1467
  • 4
    • 19344364880 scopus 로고    scopus 로고
    • Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: An overview of the randomised trials
    • Early Breast Cancer Trialists' Collaborative Group (EBCTCG).
    • Early Breast Cancer Trialists' Collaborative Group (EBCTCG). (2005) Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials. Lancet, 365, 1687-1717.
    • (2005) Lancet , vol.365 , pp. 1687-1717
  • 5
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst, J. and Kellis, M. (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol., 28, 817-825.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 6
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst, J. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 7
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • Ernst, J. and Kellis, M. (2012) ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods, 9, 215-206.
    • (2012) Nat. Methods , vol.9 , pp. 215-206
    • Ernst, J.1    Kellis, M.2
  • 10
    • 78650116700 scopus 로고    scopus 로고
    • Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data
    • Gu, F. et al. (2010) Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. BMC Syst. Biol., 4, 170.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 170
    • Gu, F.1
  • 11
    • 0030810993 scopus 로고    scopus 로고
    • Finding genes in DNA with a Hidden Markov Model
    • Henderson, J. et al. (1997) Finding genes in DNA with a hidden Markov model. J. Comput. Biol., 4, 127-141. (Pubitemid 27318310)
    • (1997) Journal of Computational Biology , vol.4 , Issue.2 , pp. 127-141
    • Henderson, J.1
  • 12
    • 33644874573 scopus 로고    scopus 로고
    • The UCSC genome browser database: Update 2006
    • Hinrichs, A.S. et al. (2005) The UCSC genome browser database: update 2006. Nucleic Acids Res., 34 (Suppl. 1), D590-D598.
    • (2005) Nucleic Acids Res. , vol.34 , Issue.SUPPL. 1
    • Hinrichs, A.S.1
  • 13
    • 77952966794 scopus 로고    scopus 로고
    • Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping
    • Hsu, P. et al. (2010) Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping. Genome Res., 20, 733-744.
    • (2010) Genome Res. , vol.20 , pp. 733-744
    • Hsu, P.1
  • 14
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang, D.W. et al. (2009a) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1
  • 15
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D.W. et al. (2009b) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc, 4, 44-57.
    • (2009) Nat. Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1
  • 18
    • 77956818209 scopus 로고    scopus 로고
    • Reversibility of pre-malignant estrogen-induced epigenetic changes
    • Kutanzi, K. et al. (2010) Reversibility of pre-malignant estrogen-induced epigenetic changes. Cell Cycle, 9, 3078-3084.
    • (2010) Cell Cycle , vol.9 , pp. 3078-3084
    • Kutanzi, K.1
  • 19
    • 79551590211 scopus 로고    scopus 로고
    • W-ChIPeaks: A comprehensive web application tool for processing ChIP-chip and ChIP-seq data
    • Lan, X. et al. (2011) W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics, 27, 428-430.
    • (2011) Bioinformatics , vol.27 , pp. 428-430
    • Lan, X.1
  • 20
    • 77954041808 scopus 로고    scopus 로고
    • HPeak: An HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
    • Qin, Z.S. et al. (2010) HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics, 11, 369.
    • (2010) BMC Bioinformatics , vol.11 , pp. 369
    • Qin, Z.S.1
  • 21
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 22
    • 79958187564 scopus 로고    scopus 로고
    • Estrogen-mediated epigenetic repression of the imprinted gene cyclin dependent kinase inhibitor 1C in breast cancer cells
    • Rodriguez, B. et al. (2011) Estrogen-mediated epigenetic repression of the imprinted gene cyclin dependent kinase inhibitor 1C in breast cancer cells. Carcinogenesis, 32, 812-821.
    • (2011) Carcinogenesis , vol.32 , pp. 812-821
    • Rodriguez, B.1
  • 24
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • Schwarz, G.E. (1978) Estimating the dimension of a model. Ann. Stat., 6, 461-464.
    • (1978) Ann. Stat. , vol.6 , pp. 461-464
    • Schwarz, G.E.1
  • 25
    • 79955690126 scopus 로고    scopus 로고
    • A modulated empirical Bayes model for identifying topological and temporal estrogen receptor a regulatory networks in breast cancer
    • Shen, C. et al. (2011) A modulated empirical Bayes model for identifying topological and temporal estrogen receptor a regulatory networks in breast cancer. BMC Syst. Biol., 5, 67.
    • (2011) BMC Syst. Biol. , vol.5 , pp. 67
    • Shen, C.1
  • 26
    • 24944555175 scopus 로고    scopus 로고
    • 16 October 2011, date last accessed
    • Smit, A. et al. (2010) RepeatMasker Open-3.0. http://www.repeatmasker.org (16 October 2011, date last accessed).
    • (2010) RepeatMasker Open-3.0
    • Smit, A.1
  • 27
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
    • Viterbi, A (1967) Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Inf. Theory, 13, 260-269.
    • (1967) IEEE Trans. Inf. Theory , vol.13 , pp. 260-269
    • Viterbi, A.1
  • 28
    • 66549085342 scopus 로고    scopus 로고
    • ChIP-Seq of ERa and RNA polymerase II defines genes differentially responding to ligands
    • Welboren, W.J. et al. (2009) ChIP-Seq of ERa and RNA polymerase II defines genes differentially responding to ligands. EMBO J., 28, 1418-1428.
    • (2009) EMBO J. , vol.28 , pp. 1418-1428
    • Welboren, W.J.1
  • 29
    • 53749092745 scopus 로고    scopus 로고
    • An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
    • Xu, H. et al. (2008) An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics, 24, 2344-2349.
    • (2008) Bioinformatics , vol.24 , pp. 2344-2349
    • Xu, H.1
  • 30
    • 78650304236 scopus 로고    scopus 로고
    • Charting histone modifications and the functional organization of mammalian genomes
    • Zhou, V.W. et al. (2011) Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet., 12, 7-18.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 7-18
    • Zhou, V.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.