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Volumn 13, Issue 2, 2009, Pages 153-164

Identifying CpG islands by different computational techniques

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; REPETITIVE DNA;

EID: 64549117398     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2008.0046     Document Type: Article
Times cited : (7)

References (43)
  • 1
    • 0026001046 scopus 로고
    • CpG islands: Features and distribution in the genomes of vertebrates
    • Aïssani, B., and Bernardi, G. (1991). CpG islands: features and distribution in the genomes of vertebrates. Gene 106, 173-183.
    • (1991) Gene , vol.106 , pp. 173-183
    • Aïssani, B.1    Bernardi, G.2
  • 2
    • 0027141519 scopus 로고
    • Number of CpG islands and genes in human and mouse
    • Antequera, F., and Bird, A. (1993). Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 90, 11995-11999.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 11995-11999
    • Antequera, F.1    Bird, A.2
  • 3
    • 0030115772 scopus 로고    scopus 로고
    • Creation of genomic methylation patterns
    • Bestor, T.H., and Tycko, B. (1996). Creation of genomic methylation patterns. Nat Genet 12, 363-367.
    • (1996) Nat Genet , vol.12 , pp. 363-367
    • Bestor, T.H.1    Tycko, B.2
  • 4
    • 0019322245 scopus 로고
    • DNA methylation and the frequency of CpG in animal DNA
    • Bird, A.P. (1980). DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8, 1499-1504.
    • (1980) Nucleic Acids Res , vol.8 , pp. 1499-1504
    • Bird, A.P.1
  • 5
    • 0022540321 scopus 로고
    • CpG-rich islands and the function of DNA methylation
    • Bird, A.P. (1986). CpG-rich islands and the function of DNA methylation. Nature 321, 209-213.
    • (1986) Nature , vol.321 , pp. 209-213
    • Bird, A.P.1
  • 6
    • 33645777446 scopus 로고    scopus 로고
    • CpG island methylation in human lymphocytes is highly correlated with DNA sequence patterns, repeat frequencies and predicted DNA structure
    • Bock, C., Paulsen, M., Tierling, S., et al. (2006). CpG island methylation in human lymphocytes is highly correlated with DNA sequence patterns, repeat frequencies and predicted DNA structure. PLoS Genet 2, e26.
    • (2006) PLoS Genet , vol.2
    • Bock, C.1    Paulsen, M.2    Tierling, S.3
  • 7
    • 34347337742 scopus 로고    scopus 로고
    • CpG island mapping by epigenome prediction
    • Bock, C., Walter, J., Paulsen, M., et al. (2007). CpG island mapping by epigenome prediction. PLoS Comput Biol 3, e110.
    • (2007) PLoS Comput Biol , vol.3
    • Bock, C.1    Walter, J.2    Paulsen, M.3
  • 8
    • 0342596934 scopus 로고
    • Sources and evolution of human Alu repeated sequences
    • Britten, R.J., Baron, W.F., Stout, D.B., et al. (1988). Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci USA 85, 4770-4774.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 4770-4774
    • Britten, R.J.1    Baron, W.F.2    Stout, D.B.3
  • 9
    • 0034017068 scopus 로고    scopus 로고
    • CpG island libraries from human chromosomes 18 and 22: Landmarks for novel genes
    • Cross, S., Clark, V.H., Simmen, M.W., et al. (2000). CpG island libraries from human chromosomes 18 and 22: landmarks for novel genes. Mamm Genome 11, 373-383.
    • (2000) Mamm Genome , vol.11 , pp. 373-383
    • Cross, S.1    Clark, V.H.2    Simmen, M.W.3
  • 10
    • 0034894297 scopus 로고    scopus 로고
    • Speciesspecific organization of CpG island promoters at mammalian homologous genes
    • Cuadrado, M., Sacristán, M., and Antequera, F. (2001). Speciesspecific organization of CpG island promoters at mammalian homologous genes. EMBO Rep 2, 586-592.
    • (2001) EMBO Rep , vol.2 , pp. 586-592
    • Cuadrado, M.1    Sacristán, M.2    Antequera, F.3
  • 12
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • Gardiner-Garden, M., and Frommer, M. (1987). CpG islands in vertebrate genomes. J Mol Biol 196, 261-282.
    • (1987) J Mol Biol , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 13
    • 36749017978 scopus 로고    scopus 로고
    • CG dinucleotide clustering is a species-specific property of the genome
    • Glass, J.L., Thompson, R.F., Khulan, B., et al. (2007). CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Res 35, 6798-6807.
    • (2007) Nucleic Acids Res , vol.35 , pp. 6798-6807
    • Glass, J.L.1    Thompson, R.F.2    Khulan, B.3
  • 14
    • 33750329496 scopus 로고    scopus 로고
    • CpGcluster: A distance-based algorithm for CpG-islands detection
    • Hackenberg, M., Previti, C., Luque-Escamilla, P.L., et al. (2006). CpGcluster: a distance-based algorithm for CpG-islands detection. BMC Bioinformat 7, 446.
    • (2006) BMC Bioinformat , vol.7 , pp. 446
    • Hackenberg, M.1    Previti, C.2    Luque-Escamilla, P.L.3
  • 15
    • 0035236049 scopus 로고    scopus 로고
    • Promoter prediction in the human genome
    • Hannenhalli, S., and Levy, S. (2001). Promoter prediction in the human genome. Bioinformatics 17 Suppl. 1, S90-S96.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Hannenhalli, S.1    Levy, S.2
  • 16
    • 33748042297 scopus 로고    scopus 로고
    • Tandem repeats in the CpG islands of imprinted genes
    • Hutter, B., Helms, V., and Paulsen, M. (2006). Tandem repeats in the CpG islands of imprinted genes. Genomics 88, 323-332.
    • (2006) Genomics , vol.88 , pp. 323-332
    • Hutter, B.1    Helms, V.2    Paulsen, M.3
  • 17
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • Hwang, D.G., and Green, P. (2004). Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA 101, 13994-14001.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 18
    • 0033822364 scopus 로고    scopus 로고
    • Large-scale human promoter mapping using CpG islands
    • Ioshikhes, I.P., and Zhang, M.Q. (2000). Large-scale human promoter mapping using CpG islands. Nat Genet 26, 61-63.
    • (2000) Nat Genet , vol.26 , pp. 61-63
    • Ioshikhes, I.P.1    Zhang, M.Q.2
  • 19
    • 0036274359 scopus 로고    scopus 로고
    • The fundamental role of epigenetic events in cancer
    • Jones, P.A., and Baylin, S.B. (2002). The fundamental role of epigenetic events in cancer. Nat Rev Genet 3, 415-426.
    • (2002) Nat Rev Genet , vol.3 , pp. 415-426
    • Jones, P.A.1    Baylin, S.B.2
  • 20
    • 0031837109 scopus 로고    scopus 로고
    • Methylated DNA and MeCP2 recruit histone deacetlyase to repress transcription
    • Jones, P.L., Veenstra, G.J.C., Wade, P.A., et al. (1998). Methylated DNA and MeCP2 recruit histone deacetlyase to repress transcription. Nat Genet 19, 187-191.
    • (1998) Nat Genet , vol.19 , pp. 187-191
    • Jones, P.L.1    Veenstra, G.J.C.2    Wade, P.A.3
  • 21
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander, E.S., Linton, L.M., Birren, B., et al. (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1    Linton, L.M.2    Birren, B.3
  • 22
    • 0026742792 scopus 로고
    • CpG islands as gene markers in the human genome
    • Larsen, F., Gundersen, G., Lopez, R., et al. (1992). CpG islands as gene markers in the human genome. Genomics 13, 1095-1107.
    • (1992) Genomics , vol.13 , pp. 1095-1107
    • Larsen, F.1    Gundersen, G.2    Lopez, R.3
  • 23
    • 0035984483 scopus 로고    scopus 로고
    • Applications of recursive segmentation to the analysis of DNA sequences
    • Li, W., Bernaola-Galván, P., Haghighi, F., et al. (2002). Applications of recursive segmentation to the analysis of DNA sequences. Comput Chem 26, 491-510.
    • (2002) Comput Chem , vol.26 , pp. 491-510
    • Li, W.1    Bernaola-Galván, P.2    Haghighi, F.3
  • 25
    • 0027893006 scopus 로고
    • Evidence for erosion of mouse CpG islands during mammalian evolution
    • Matsuo, K., Clay, O., Takahashi, T., et al. (1993). Evidence for erosion of mouse CpG islands during mammalian evolution. Som Cell Mol Gen 19, 543-555.
    • (1993) Som Cell Mol Gen , vol.19 , pp. 543-555
    • Matsuo, K.1    Clay, O.2    Takahashi, T.3
  • 26
    • 0035999991 scopus 로고    scopus 로고
    • CpGProD: Identifying CpG islands associated with transcription start sites in large genomic mammalian sequences
    • Ponger, L., and Mouchiroud, D. (2001). CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics 18, 631-633.
    • (2001) Bioinformatics , vol.18 , pp. 631-633
    • Ponger, L.1    Mouchiroud, D.2
  • 27
    • 0035183199 scopus 로고    scopus 로고
    • Determinants of CpG islands: Expression in early embryo and isochore structure
    • Ponger, L., Duret, L., and Mouchiroud, D. (2001). Determinants of CpG islands: expression in early embryo and isochore structure. Genome Res 11, 1854-1860.
    • (2001) Genome Res , vol.11 , pp. 1854-1860
    • Ponger, L.1    Duret, L.2    Mouchiroud, D.3
  • 28
    • 0028291115 scopus 로고
    • A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes
    • Quentin, Y. (1994). A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes. Nucleic Acids Res 22, 2222-2227.
    • (1994) Nucleic Acids Res , vol.22 , pp. 2222-2227
    • Quentin, Y.1
  • 29
    • 0035234557 scopus 로고    scopus 로고
    • Genomic imprinting: Parental influence on the genome
    • Reik, W., and Walter, J. (2001). Genomic imprinting: parental influence on the genome. Nat Rev Genet 2, 21-32.
    • (2001) Nat Rev Genet , vol.2 , pp. 21-32
    • Reik, W.1    Walter, J.2
  • 30
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • Rice, P., Longden, I., and Bleasby, A. (2000). EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16, 276-277.
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 31
    • 0034305821 scopus 로고    scopus 로고
    • DNA methylation in health and disease
    • Robertson, K.D., and Wolffe, A.P. (2000). DNA methylation in health and disease. Nat Rev Genet 1, 11-19.
    • (2000) Nat Rev Genet , vol.1 , pp. 11-19
    • Robertson, K.D.1    Wolffe, A.P.2
  • 32
    • 0032531815 scopus 로고    scopus 로고
    • Does SINE evolution peclude Alu function?
    • Schmid, C.W. (1998). Does SINE evolution peclude Alu function? Nucleic Acids Res 26, 4541-4550.
    • (1998) Nucleic Acids Res , vol.26 , pp. 4541-4550
    • Schmid, C.W.1
  • 33
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • Shannon, C.E. (1948). A mathematical theory of communication. Bell Sys Tech J 27, 379-423, 623-656.
    • (1948) Bell Sys Tech J , vol.27 , Issue.379-423 , pp. 623-656
    • Shannon, C.E.1
  • 34
    • 14744267496 scopus 로고    scopus 로고
    • Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression
    • Song, F., Smith, J.F., Kimura, M.T., et al. (2005). Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci USA 102, 3336-3341.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 3336-3341
    • Song, F.1    Smith, J.F.2    Kimura, M.T.3
  • 35
    • 0036230566 scopus 로고    scopus 로고
    • A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes
    • Strichman-Almashanu, L.Z., Lee, R.S., Onyango, P.O., et al. (2002). A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. Genome Res 12, 543-554.
    • (2002) Genome Res , vol.12 , pp. 543-554
    • Strichman-Almashanu, L.Z.1    Lee, R.S.2    Onyango, P.O.3
  • 36
    • 0037133565 scopus 로고    scopus 로고
    • Comprehensive analysis of CpG islands in human chromosomes 21 and 22
    • Takai, D., and Jones, P.A. (2002). Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99, 3740-3745.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 3740-3745
    • Takai, D.1    Jones, P.A.2
  • 37
    • 0025266610 scopus 로고
    • Alternative chromatin structure at CpG islands
    • Tazi, J., and Bird, A.P. (1990). Alternative chromatin structure at CpG islands. Cell 60, 909-920.
    • (1990) Cell , vol.60 , pp. 909-920
    • Tazi, J.1    Bird, A.P.2
  • 38
    • 2442684104 scopus 로고    scopus 로고
    • An evaluation of new criteria for CpG islands in the human genome as gene markers
    • Wang, Y., and Leung, F.C.C. (2004). An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics 20, 1170-1177.
    • (2004) Bioinformatics , vol.20 , pp. 1170-1177
    • Wang, Y.1    Leung, F.C.C.2
  • 39
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston, R.H., Lindblad-Toh, K., Birney, E., et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1    Lindblad-Toh, K.2    Birney, E.3
  • 40
    • 1242296842 scopus 로고    scopus 로고
    • A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q
    • Yamada, Y., Watanabe, H., Miura, F., et al. (2004). A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res 14, 274-266.
    • (2004) Genome Res , vol.14 , pp. 274-266
    • Yamada, Y.1    Watanabe, H.2    Miura, F.3
  • 41
    • 19344368143 scopus 로고    scopus 로고
    • Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity
    • Yamashita, R., Suzuki, Y., Sugano, S., et al. (2005). Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 350, 129-136.
    • (2005) Gene , vol.350 , pp. 129-136
    • Yamashita, R.1    Suzuki, Y.2    Sugano, S.3
  • 42
    • 29344432096 scopus 로고    scopus 로고
    • Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences
    • Zhao, Z., and Zhang, F. (2006a). Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences. Genomics 87, 68-74.
    • (2006) Genomics , vol.87 , pp. 68-74
    • Zhao, Z.1    Zhang, F.2
  • 43
    • 32444436681 scopus 로고    scopus 로고
    • Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome
    • Zhao, Z., and Zhang, F. (2006b). Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome. Gene 366, 316-324.
    • (2006) Gene , vol.366 , pp. 316-324
    • Zhao, Z.1    Zhang, F.2


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