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Volumn 9, Issue 9, 2013, Pages

Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CORRELATION METHODS; CYTOLOGY;

EID: 84884697780     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003168     Document Type: Article
Times cited : (32)

References (55)
  • 1
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin Modifications and Their Function
    • Kouzarides T, (2007) Chromatin Modifications and Their Function. Cell 128: 693-705.
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 2
    • 79959484677 scopus 로고    scopus 로고
    • Signals and Combinatorial Functions of Histone Modifications
    • Suganuma T, Workman JL, (2011) Signals and Combinatorial Functions of Histone Modifications. Annual Review Biochemistry 80: 473-499.
    • (2011) Annual Review Biochemistry , vol.80 , pp. 473-499
    • Suganuma, T.1    Workman, J.L.2
  • 3
    • 0035839136 scopus 로고    scopus 로고
    • Translating the histone code
    • Jenuwein T, Allis CD, (2001) Translating the histone code. Science 293: 1074-1080.
    • (2001) Science , vol.293 , pp. 1074-1080
    • Jenuwein, T.1    Allis, C.D.2
  • 4
    • 33847070442 scopus 로고    scopus 로고
    • The role of chromatin during transcription
    • Li B, Carey M, Workman JL, (2007) The role of chromatin during transcription. Cell 128: 707-719.
    • (2007) Cell , vol.128 , pp. 707-719
    • Li, B.1    Carey, M.2    Workman, J.L.3
  • 5
    • 34249299791 scopus 로고    scopus 로고
    • The complex language of chromatin regulation during transcription
    • Berger SL, (2007) The complex language of chromatin regulation during transcription. Nature 447: 407-412.
    • (2007) Nature , vol.447 , pp. 407-412
    • Berger, S.L.1
  • 6
    • 34249026300 scopus 로고    scopus 로고
    • High-Resolution Profiling of Histone Methylations in the Human Genome
    • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-Resolution Profiling of Histone Methylations in the Human Genome. Cell 129: 823-837.
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.Y.4    Schones, D.E.5
  • 7
    • 46249112085 scopus 로고    scopus 로고
    • Combinatorial patterns of histone acetylations and methylations in the human genome
    • Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics 40: 897-903.
    • (2008) Nature Genetics , vol.40 , pp. 897-903
    • Wang, Z.1    Zang, C.2    Rosenfeld, J.A.3    Schones, D.E.4    Barski, A.5
  • 8
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-type-specific gene expression
    • Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1    Hon, G.C.2    Hawkins, R.D.3    Kheradpour, P.4    Stark, A.5
  • 9
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst J, Kellis M, (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotechnology 28: 817-825.
    • (2010) Nature Biotechnology , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 10
    • 79953233745 scopus 로고    scopus 로고
    • Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information
    • Wang J, (2011) Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information. BMC Genomics 12: 172.
    • (2011) BMC Genomics , vol.12 , pp. 172
    • Wang, J.1
  • 11
    • 77649177097 scopus 로고    scopus 로고
    • Predictive chromatin signatures in the mammalian genome
    • Hon GC, Hawkins RD, Ren B, (2009) Predictive chromatin signatures in the mammalian genome. Human Molecular Genetics 18: R195-R201.
    • (2009) Human Molecular Genetics , vol.18
    • Hon, G.C.1    Hawkins, R.D.2    Ren, B.3
  • 13
    • 62849085018 scopus 로고    scopus 로고
    • Prediction of regulatory elements in mammalian genomes using chromatin signatures
    • Won KJ, Chepelev I, Ren B, Wang W, (2008) Prediction of regulatory elements in mammalian genomes using chromatin signatures. BMC Bioinformatics 9: 547.
    • (2008) BMC Bioinformatics , vol.9 , pp. 547
    • Won, K.J.1    Chepelev, I.2    Ren, B.3    Wang, W.4
  • 14
    • 59949103192 scopus 로고    scopus 로고
    • High-resolution human core-promoter prediction with CoreBoost HM
    • Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ, (2009) High-resolution human core-promoter prediction with CoreBoost HM. Genome Research 19: 266-275.
    • (2009) Genome Research , vol.19 , pp. 266-275
    • Wang, X.1    Xuan, Z.2    Zhao, X.3    Li, Y.4    Zhang, M.Q.5
  • 15
    • 77349120278 scopus 로고    scopus 로고
    • Genome-wide prediction of transcription factor binding sites using an integrated model
    • Won KJ, Ren B, Wang W, (2010) Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biology 11: R7.
    • (2010) Genome Biology , vol.11
    • Won, K.J.1    Ren, B.2    Wang, W.3
  • 16
    • 80051949745 scopus 로고    scopus 로고
    • Tissue-specific prediction of directly regulated genes
    • McLeay RC, Leat CJ, Bailey TL, (2011) Tissue-specific prediction of directly regulated genes. Bioinformatics 27: 2354-2360.
    • (2011) Bioinformatics , vol.27 , pp. 2354-2360
    • McLeay, R.C.1    Leat, C.J.2    Bailey, T.L.3
  • 17
    • 79955807556 scopus 로고    scopus 로고
    • Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes
    • Zhang Z, Zhang MQ, (2011) Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics 12: 155.
    • (2011) BMC Bioinformatics , vol.12 , pp. 155
    • Zhang, Z.1    Zhang, M.Q.2
  • 19
    • 48949099045 scopus 로고    scopus 로고
    • Inferring causal relationships among different histone modifications and gene expression
    • Yu H, Zhu S, Zhou B, Xue H, Han JDJ, (2008) Inferring causal relationships among different histone modifications and gene expression. Genome Research 18: 1314-1324.
    • (2008) Genome Research , vol.18 , pp. 1314-1324
    • Yu, H.1    Zhu, S.2    Zhou, B.3    Xue, H.4    Han, J.D.J.5
  • 20
    • 67649476233 scopus 로고    scopus 로고
    • Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale-free network
    • Hayashi Y, Senda T, Sano N, Horikoshi M, (2009) Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale-free network. Genes Cells 14: 789-806.
    • (2009) Genes Cells , vol.14 , pp. 789-806
    • Hayashi, Y.1    Senda, T.2    Sano, N.3    Horikoshi, M.4
  • 21
    • 78649782638 scopus 로고    scopus 로고
    • Regulatory Patterns of Histone Modifications to Control the DNA Methylation Status at CpG Islands
    • Jung I, Kim D, (2009) Regulatory Patterns of Histone Modifications to Control the DNA Methylation Status at CpG Islands. Interdisciplinary Bio Central 1: 1-8.
    • (2009) Interdisciplinary Bio Central , vol.1 , pp. 1-8
    • Jung, I.1    Kim, D.2
  • 23
    • 80052297897 scopus 로고    scopus 로고
    • Combinatorial patterns of histone modifications in Saccharomyces.cerevisiae
    • Cui XJ, Li H, Liu GQ, (2011) Combinatorial patterns of histone modifications in Saccharomyces.cerevisiae. Yeast 28: 683-691.
    • (2011) Yeast , vol.28 , pp. 683-691
    • Cui, X.J.1    Li, H.2    Liu, G.Q.3
  • 25
    • 0004213845 scopus 로고    scopus 로고
    • Cambridge University Press
    • Pearl J (2000) Causality. Cambridge University Press.
    • (2000) Causality
    • Pearl, J.1
  • 26
    • 0039289571 scopus 로고    scopus 로고
    • What is wrong with Bayes nets
    • Cartwright N, (2001) What is wrong with Bayes nets? The Monist 84: 242-264.
    • (2001) The Monist , vol.84 , pp. 242-264
    • Cartwright, N.1
  • 29
    • 0001038826 scopus 로고
    • Covariance selection
    • Dempster AP, (1972) Covariance selection. Biometrics 28: 157-175.
    • (1972) Biometrics , vol.28 , pp. 157-175
    • Dempster, A.P.1
  • 36
    • 0032808670 scopus 로고    scopus 로고
    • The insignificance of statistical significance testing
    • Johnson D, (1999) The insignificance of statistical significance testing. Journal of Wildlife Management 63: 763-772.
    • (1999) Journal of Wildlife Management , vol.63 , pp. 763-772
    • Johnson, D.1
  • 38
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCylopedia Of DNA Elements) Project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium (2004) The ENCODE (ENCylopedia Of DNA Elements) Project. Science 306: 636-640.
    • (2004) Science , vol.306 , pp. 636-640
  • 39
    • 61349098460 scopus 로고    scopus 로고
    • Differential chromatin marking of introns and expressed exons by H3K36me3
    • Kolasinska-Zwierz1 P, Down1 T, Latorre I, Liu T, Liu XS, et al. (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nature Genetics 41: 376-381.
    • (2009) Nature Genetics , vol.41 , pp. 376-381
    • Kolasinska-Zwierz, P.1    Downa, T.2    Latorre, I.3    Liu, T.4    Liu, X.S.5
  • 40
    • 59949085939 scopus 로고    scopus 로고
    • H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
    • Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, et al. (2009) H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Research 19: 221-233.
    • (2009) Genome Research , vol.19 , pp. 221-233
    • Pauler, F.M.1    Sloane, M.A.2    Huang, R.3    Regha, K.4    Koerner, M.V.5
  • 41
    • 34248171732 scopus 로고    scopus 로고
    • The polycomb group protein SUZ12 regulates histone H3 lysine 9 methylation and HP1 alpha distribution
    • de la Cruz CC, Kirmizis A, Simon MD, Isono K, Koseki H, et al. (2007) The polycomb group protein SUZ12 regulates histone H3 lysine 9 methylation and HP1 alpha distribution. Chromosome Research 15: 299-314.
    • (2007) Chromosome Research , vol.15 , pp. 299-314
    • de la Cruz, C.C.1    Kirmizis, A.2    Simon, M.D.3    Isono, K.4    Koseki, H.5
  • 42
    • 77957369358 scopus 로고    scopus 로고
    • Histone H2B ubiquitination and beyond: Regulation of nucleosome stability, chromatin dynamics and the trans-histone H3 methylation
    • Chandrasekharan MB, Huang F, Sun ZW, (2010) Histone H2B ubiquitination and beyond: Regulation of nucleosome stability, chromatin dynamics and the trans-histone H3 methylation. Epigenetics 5: 460-468.
    • (2010) Epigenetics , vol.5 , pp. 460-468
    • Chandrasekharan, M.B.1    Huang, F.2    Sun, Z.W.3
  • 45
    • 84876384807 scopus 로고    scopus 로고
    • Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication
    • na Diaz JP, Hegre SA, Anderssen E, Aas PA, Mjelle R, et al. (2013) Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication. Nucleic Acids Research 41: 846-2856.
    • (2013) Nucleic Acids Research , vol.41 , pp. 846-2856
    • Diaz, J.P.1    Hegre, S.A.2    Anderssen, E.3    Aas, P.A.4    Mjelle, R.5
  • 47
    • 77956643239 scopus 로고    scopus 로고
    • Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers
    • Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, et al. (2010) Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 142: 967-980.
    • (2010) Cell , vol.142 , pp. 967-980
    • Vermeulen, M.1    Eberl, H.C.2    Matarese, F.3    Marks, H.4    Denissov, S.5
  • 48
    • 84455200582 scopus 로고    scopus 로고
    • Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
    • Ram O, Goren A, Amit I, Shoresh N, Yosef N, et al. (2011) Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 147: 1628-1639.
    • (2011) Cell , vol.147 , pp. 1628-1639
    • Ram, O.1    Goren, A.2    Amit, I.3    Shoresh, N.4    Yosef, N.5
  • 49
    • 84884682035 scopus 로고    scopus 로고
    • DNA Nexus, Available
    • DNA Nexus (2012). Sequence Read Archive. Available: http://sra.dnanexus.com/experiments/.
    • (2012) Sequence Read Archive
  • 50
    • 84884683565 scopus 로고    scopus 로고
    • San Diego Epigenome Center, Available
    • San Diego Epigenome Center (2012). Antibody Validation. Available: http://epigenome.ucsd.edu/antibodies.html.
    • (2012) Antibody Validation
  • 51
    • 84884694460 scopus 로고    scopus 로고
    • Harvard Medical School, Available
    • Harvard Medical School (2012). Antibody Validation Database. Available: http://compbio.med.harvard.edu/antibodies/sources/.
    • (2012) Antibody Validation Database
  • 52
    • 0001165055 scopus 로고
    • Frequency distribution of the values of the correlation coefficient in samples of an indefinitely large population
    • Fisher RA, (1915) Frequency distribution of the values of the correlation coefficient in samples of an indefinitely large population. Biometrika 10: 507-521.
    • (1915) Biometrika , vol.10 , pp. 507-521
    • Fisher, R.A.1
  • 53
    • 45849134070 scopus 로고    scopus 로고
    • Sparse inverse covariance estimation with the graphical lasso
    • Friedman J, Hastie T, Tibshirani R, (2008) Sparse inverse covariance estimation with the graphical lasso. Biostatistics 9: 432-441.
    • (2008) Biostatistics , vol.9 , pp. 432-441
    • Friedman, J.1    Hastie, T.2    Tibshirani, R.3
  • 54
    • 41549101939 scopus 로고    scopus 로고
    • Model Selection Through Sparse Maximum Likelihood Estimation for Multivariate Gaussian or Binary Data
    • Banerjee O, El Ghaoui L, d'Aspremont A, (2008) Model Selection Through Sparse Maximum Likelihood Estimation for Multivariate Gaussian or Binary Data. Journal of Machine Learning Research 9: 485-516.
    • (2008) Journal of Machine Learning Research , vol.9 , pp. 485-516
    • Banerjee, O.1    El Ghaoui, L.2    d'Aspremont, A.3


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