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Volumn 366, Issue 2, 2006, Pages 316-324

Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome

Author keywords

CpG dinucleotide; CpG islands; GC content; Short sequence; SNPs

Indexed keywords

ARTICLE; CPG ISLAND; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCATION; GENE MUTATION; GENE REPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENOMICS; HUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 32444436681     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2005.08.024     Document Type: Article
Times cited : (32)

References (29)
  • 1
    • 2142814375 scopus 로고    scopus 로고
    • Methylomics in psychiatry: Modulation of gene-environment interactions may be through DNA methylation
    • H.M. Abdolmaleky Methylomics in psychiatry: modulation of gene-environment interactions may be through DNA methylation Am. J. Med. Genet., Part B Neuropsychiatr. Genet. 127 2004 51 59
    • (2004) Am. J. Med. Genet., Part B Neuropsychiatr. Genet. , vol.127 , pp. 51-59
    • Abdolmaleky, H.M.1
  • 2
    • 0027141519 scopus 로고
    • Number of CpG islands and genes in human and mouse
    • F. Antequera, and A. Bird Number of CpG islands and genes in human and mouse Proc. Natl. Acad. Sci. U. S. A. 90 1993 11995 11999
    • (1993) Proc. Natl. Acad. Sci. U. S. A. , vol.90 , pp. 11995-11999
    • Antequera, F.1    Bird, A.2
  • 3
    • 0042329754 scopus 로고    scopus 로고
    • Structure, function and evolution of CpG island promoters
    • F. Antequera Structure, function and evolution of CpG island promoters Cell. Mol. Life Sci. 60 2003 1647 1658
    • (2003) Cell. Mol. Life Sci. , vol.60 , pp. 1647-1658
    • Antequera, F.1
  • 4
    • 0026631005 scopus 로고
    • The influence of nearest neighbors on the rate and pattern of spontaneous point mutations
    • R.D. Blake, S.T. Hess, and J. Nicholson-Tuell The influence of nearest neighbors on the rate and pattern of spontaneous point mutations J. Mol. Evol. 34 1992 189 200
    • (1992) J. Mol. Evol. , vol.34 , pp. 189-200
    • Blake, R.D.1    Hess, S.T.2    Nicholson-Tuell, J.3
  • 5
    • 0034084035 scopus 로고    scopus 로고
    • Analysis of expressed sequence tags indicates 35,000 human genes
    • B. Ewing, and P. Green Analysis of expressed sequence tags indicates 35,000 human genes Nat. Genet. 25 2000 232 234
    • (2000) Nat. Genet. , vol.25 , pp. 232-234
    • Ewing, B.1    Green, P.2
  • 6
    • 0142092542 scopus 로고    scopus 로고
    • Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population
    • Y. Freudenberg-Hua Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population Genome Res. 13 2003 2271 2276
    • (2003) Genome Res. , vol.13 , pp. 2271-2276
    • Freudenberg-Hua, Y.1
  • 7
    • 0033858879 scopus 로고    scopus 로고
    • Cytosine deamination plays a primary role in the evolution of mammalian isochores
    • K.J. Fryxell, and E. Zuckerkandl Cytosine deamination plays a primary role in the evolution of mammalian isochores Mol. Biol. Evol. 17 2000 1371 1383
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1371-1383
    • Fryxell, K.J.1    Zuckerkandl, E.2
  • 8
    • 14544298936 scopus 로고    scopus 로고
    • CpG mutation rates in the human genome are highly dependent on local GC content
    • K.J. Fryxell, and W.J. Moon CpG mutation rates in the human genome are highly dependent on local GC content Mol. Biol. Evol. 22 2005 650 658
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 650-658
    • Fryxell, K.J.1    Moon, W.J.2
  • 9
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • M. Gardiner-Garden, and M. Frommer CpG islands in vertebrate genomes J. Mol. Biol. 196 1987 261 282
    • (1987) J. Mol. Biol. , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 10
    • 0028294455 scopus 로고
    • Wide variations in neighbor-dependent substitution rates
    • S.T. Hess, J.D. Blake, and R.D. Blake Wide variations in neighbor-dependent substitution rates J. Mol. Biol. 236 1994 1022 1033
    • (1994) J. Mol. Biol. , vol.236 , pp. 1022-1033
    • Hess, S.T.1    Blake, J.D.2    Blake, R.D.3
  • 11
    • 0032231701 scopus 로고    scopus 로고
    • Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes
    • M. Krawczak, E.V. Ball, and D.N. Cooper Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes Am. J. Hum. Genet. 63 1998 474 488
    • (1998) Am. J. Hum. Genet. , vol.63 , pp. 474-488
    • Krawczak, M.1    Ball, E.V.2    Cooper, D.N.3
  • 12
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • E.S. Lander Initial sequencing and analysis of the human genome Nature 409 2001 860 921
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 13
    • 0026742792 scopus 로고
    • CpG islands as gene markers in the human genome
    • F. Larsen, G. Gundersen, R. Lopez, and H. Prydz CpG islands as gene markers in the human genome Genomics 13 1992 1095 1107
    • (1992) Genomics , vol.13 , pp. 1095-1107
    • Larsen, F.1    Gundersen, G.2    Lopez, R.3    Prydz, H.4
  • 14
    • 0021710490 scopus 로고
    • Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications
    • W.H. Li, C.I. Wu, and C.C. Luo Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications J. Mol. Evol. 21 1984 58 71
    • (1984) J. Mol. Evol. , vol.21 , pp. 58-71
    • Li, W.H.1    Wu, C.I.2    Luo, C.C.3
  • 15
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer Associates Sunderland, MA
    • W.-H. Li Molecular Evolution 1997 Sinauer Associates Sunderland, MA
    • (1997) Molecular Evolution
    • Li, W.-H.1
  • 16
    • 0035999991 scopus 로고    scopus 로고
    • CpGProD: Identifying CpG islands associated with transcription start sites in large genomic mammalian sequences
    • L. Ponger, and D. Mouchiroud CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences Bioinformatics 18 2002 631 633
    • (2002) Bioinformatics , vol.18 , pp. 631-633
    • Ponger, L.1    Mouchiroud, D.2
  • 17
    • 0035183199 scopus 로고    scopus 로고
    • Determinants of CpG islands: Expression in early embryo and isochore structure
    • L. Ponger, L. Duret, and D. Mouchiroud Determinants of CpG islands: expression in early embryo and isochore structure Genome Res. 11 2001 1854 1860
    • (2001) Genome Res. , vol.11 , pp. 1854-1860
    • Ponger, L.1    Duret, L.2    Mouchiroud, D.3
  • 18
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
    • A. Siepel, and D. Haussler Phylogenetic estimation of context-dependent substitution rates by maximum likelihood Mol. Biol. Evol. 21 2004 468 488
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 468-488
    • Siepel, A.1    Haussler, D.2
  • 19
    • 0025299347 scopus 로고
    • The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model
    • J. Sved, and A. Bird The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model Proc. Natl. Acad. Sci. U. S. A. 87 1990 4692 4696
    • (1990) Proc. Natl. Acad. Sci. U. S. A. , vol.87 , pp. 4692-4696
    • Sved, J.1    Bird, A.2
  • 20
    • 0037133565 scopus 로고    scopus 로고
    • Comprehensive analysis of CpG islands in human chromosomes 21 and 22
    • D. Takai, and P.A. Jones Comprehensive analysis of CpG islands in human chromosomes 21 and 22 Proc. Natl. Acad. Sci. U. S. A. 99 2002 3740 3745
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 3740-3745
    • Takai, D.1    Jones, P.A.2
  • 21
    • 0345603004 scopus 로고    scopus 로고
    • The CpG island searcher: A new WWW resource
    • D. Takai, and P.A. Jones The CpG island searcher: a new WWW resource In Silico Biol. 3 2003 235 240
    • (2003) In Silico Biol. , vol.3 , pp. 235-240
    • Takai, D.1    Jones, P.A.2
  • 22
    • 0037459252 scopus 로고    scopus 로고
    • Sequence context at human single nucleotide polymorphisms: Overrepresentation of CpG dinucleotide at polymorphic sites and suppression of variation in CpG islands
    • D.J. Tomso, and D.A. Bell Sequence context at human single nucleotide polymorphisms: overrepresentation of CpG dinucleotide at polymorphic sites and suppression of variation in CpG islands J. Mol. Biol. 327 2003 303 308
    • (2003) J. Mol. Biol. , vol.327 , pp. 303-308
    • Tomso, D.J.1    Bell, D.A.2
  • 23
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • J.C. Venter The sequence of the human genome Science 291 2001 1304 1351
    • (2001) Science , vol.291 , pp. 1304-1351
    • Venter, J.C.1
  • 24
    • 2442684104 scopus 로고    scopus 로고
    • An evaluation of new criteria for CpG islands in the human genome as gene markers
    • Y. Wang, and F.C. Leung An evaluation of new criteria for CpG islands in the human genome as gene markers Bioinformatics 20 2004 1170 1177
    • (2004) Bioinformatics , vol.20 , pp. 1170-1177
    • Wang, Y.1    Leung, F.C.2
  • 25
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • R.H. Waterston Initial sequencing and comparative analysis of the mouse genome Nature 420 2002 520 562
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1
  • 26
    • 13444293344 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • D.L. Wheeler Database resources of the National Center for Biotechnology Information Nucleic Acids Res. 33 2005 D39 D45
    • (2005) Nucleic Acids Res. , vol.33
    • Wheeler, D.L.1
  • 27
    • 4744359031 scopus 로고    scopus 로고
    • The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs
    • F. Zhang, and Z. Zhao The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs Genomics 84 2004 785 795
    • (2004) Genomics , vol.84 , pp. 785-795
    • Zhang, F.1    Zhao, Z.2
  • 28
    • 0036852246 scopus 로고    scopus 로고
    • Neighboring-nucleotide effects on single nucleotide polymorphisms: A study of 2.6 million polymorphisms across the human genome
    • Z. Zhao, and E. Boerwinkle Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome Genome Res. 12 2002 1679 1686
    • (2002) Genome Res. , vol.12 , pp. 1679-1686
    • Zhao, Z.1    Boerwinkle, E.2
  • 29
    • 0141541805 scopus 로고    scopus 로고
    • Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution
    • Z. Zhao, Y.-X. Fu, D. Hewett-Emmett, and E. Boerwinkle Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution Gene 312 2003 207 213
    • (2003) Gene , vol.312 , pp. 207-213
    • Zhao, Z.1    Fu, Y.-X.2    Hewett-Emmett, D.3    Boerwinkle, E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.