메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Estimation of CpG coverage in whole methylome next-generation sequencing studies

Author keywords

Association studies; MBD MeDIP; Methylation; Next generation sequencing

Indexed keywords

COST-EFFECTIVE APPROACH; FRAGMENT SIZE DISTRIBUTION; GENETIC STUDIES; HIGHLY ACCURATE; INTER-INDIVIDUAL DIFFERENCES; MBD/MEDIP; METHYLATED DNAS; NEXT-GENERATION SEQUENCING; NONPARAMETRIC METHODS;

EID: 84873700342     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-50     Document Type: Article
Times cited : (25)

References (35)
  • 1
    • 0035839126 scopus 로고    scopus 로고
    • Epigenetic reprogramming in mammalian development
    • 10.1126/science.1063443, 11498579
    • Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001, 293(5532):1089-1093. 10.1126/science.1063443, 11498579.
    • (2001) Science , vol.293 , Issue.5532 , pp. 1089-1093
    • Reik, W.1    Dean, W.2    Walter, J.3
  • 2
    • 77953469917 scopus 로고    scopus 로고
    • Epigenetics as a unifying principle in the aetiology of complex traits and diseases
    • 10.1038/nature09230, 20535201
    • Petronis A. Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 2010, 465(7299):721-727. 10.1038/nature09230, 20535201.
    • (2010) Nature , vol.465 , Issue.7299 , pp. 721-727
    • Petronis, A.1
  • 3
    • 0347123629 scopus 로고    scopus 로고
    • Early nutrition, epigenetic changes at transposons and imprinted genes, and enhanced susceptibility to adult chronic diseases
    • 10.1016/j.nut.2003.09.011, 14698016
    • Waterland RA, Jirtle RL. Early nutrition, epigenetic changes at transposons and imprinted genes, and enhanced susceptibility to adult chronic diseases. Nutrition 2004, 20(1):63-68. 10.1016/j.nut.2003.09.011, 14698016.
    • (2004) Nutrition , vol.20 , Issue.1 , pp. 63-68
    • Waterland, R.A.1    Jirtle, R.L.2
  • 4
    • 0026005763 scopus 로고
    • Estradiol down regulates the binding activity of an avian vitellogenin gene repressor (MDBP-2) and triggers a gradual demethylation of the mCpG pair of its DNA binding site
    • 10.1093/nar/19.20.5771, 328989, 1945854
    • Jost JP, Saluz HP, Pawlak A. Estradiol down regulates the binding activity of an avian vitellogenin gene repressor (MDBP-2) and triggers a gradual demethylation of the mCpG pair of its DNA binding site. Nucleic Acids Res 1991, 19(20):5771-5775. 10.1093/nar/19.20.5771, 328989, 1945854.
    • (1991) Nucleic Acids Res , vol.19 , Issue.20 , pp. 5771-5775
    • Jost, J.P.1    Saluz, H.P.2    Pawlak, A.3
  • 5
    • 0028966928 scopus 로고
    • Sexually dimorphic DNA demethylation in the promoter of the Slp (sex-limited protein) gene in mouse liver
    • Yokomori N, Moore R, Negishi M. Sexually dimorphic DNA demethylation in the promoter of the Slp (sex-limited protein) gene in mouse liver. ProcNatlAcadSciUSA 1995, 92(5):1302-1306.
    • (1995) ProcNatlAcadSciUSA , vol.92 , Issue.5 , pp. 1302-1306
    • Yokomori, N.1    Moore, R.2    Negishi, M.3
  • 6
    • 0037354521 scopus 로고    scopus 로고
    • Epigenetics and the environment
    • Sutherland JE, Costa M. Epigenetics and the environment. AnnNYAcadSci 2003, 983:151-160.
    • (2003) AnnNYAcadSci , vol.983 , pp. 151-160
    • Sutherland, J.E.1    Costa, M.2
  • 7
    • 0027458127 scopus 로고
    • Are somatic cells inherently deficient in methylation metabolism? A proposed mechanism for DNA methylation loss, senescence and aging
    • Cooney CA. Are somatic cells inherently deficient in methylation metabolism? A proposed mechanism for DNA methylation loss, senescence and aging. Growth Dev Aging 1993, 57(4):261-273.
    • (1993) Growth Dev Aging , vol.57 , Issue.4 , pp. 261-273
    • Cooney, C.A.1
  • 8
    • 0033988813 scopus 로고    scopus 로고
    • DNA methyltransferase Dnmt1 associates with histone deacetylase activity
    • 10.1038/71750, 10615135
    • Fuks F, Burgers WA, Brehm A, Hughes-Davies L, Kouzarides T. DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nat Genet 2000, 24(1):88-91. 10.1038/71750, 10615135.
    • (2000) Nat Genet , vol.24 , Issue.1 , pp. 88-91
    • Fuks, F.1    Burgers, W.A.2    Brehm, A.3    Hughes-Davies, L.4    Kouzarides, T.5
  • 9
    • 0038576158 scopus 로고    scopus 로고
    • The power and the promise of DNA methylation markers
    • Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer 2003, 3:253-266.
    • (2003) Nat Rev Cancer , vol.3 , pp. 253-266
    • Laird, P.W.1
  • 10
    • 55449120805 scopus 로고    scopus 로고
    • Genetic mapping in human disease
    • 10.1126/science.1156409, 2694957, 18988837
    • Altshuler D, Daly MJ, Lander ES. Genetic mapping in human disease. Science 2008, 322(5903):881-888. 10.1126/science.1156409, 2694957, 18988837.
    • (2008) Science , vol.322 , Issue.5903 , pp. 881-888
    • Altshuler, D.1    Daly, M.J.2    Lander, E.S.3
  • 11
    • 79960556965 scopus 로고    scopus 로고
    • Epigenome-wide association studies for common human diseases
    • 10.1038/nrg3000, 3508712, 21747404
    • Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet 2011, 12(8):529-541. 10.1038/nrg3000, 3508712, 21747404.
    • (2011) Nat Rev Genet , vol.12 , Issue.8 , pp. 529-541
    • Rakyan, V.K.1    Down, T.A.2    Balding, D.J.3    Beck, S.4
  • 12
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide DNA methylation analysis
    • Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010, 11(3):191-203.
    • (2010) Nat Rev Genet , vol.11 , Issue.3 , pp. 191-203
    • Laird, P.W.1
  • 13
    • 42649089780 scopus 로고    scopus 로고
    • The methylome: approaches for global DNA methylation profiling
    • 10.1016/j.tig.2008.01.006, 18325624
    • Beck S, Rakyan VK. The methylome: approaches for global DNA methylation profiling. Trends Genet 2008, 24(5):231-237. 10.1016/j.tig.2008.01.006, 18325624.
    • (2008) Trends Genet , vol.24 , Issue.5 , pp. 231-237
    • Beck, S.1    Rakyan, V.K.2
  • 14
    • 66449121652 scopus 로고    scopus 로고
    • Finding the fifth base: genome-wide sequencing of cytosine methylation
    • 10.1101/gr.083451.108, 19273618
    • Lister R, Ecker JR. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 2009, 19(6):959-966. 10.1101/gr.083451.108, 19273618.
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 959-966
    • Lister, R.1    Ecker, J.R.2
  • 15
    • 78649969065 scopus 로고    scopus 로고
    • The DNA methylome of human peripheral blood mononuclear cells
    • 10.1371/journal.pbio.1000533, 2976721, 21085693
    • Li Y, Zhu J, Tian G, Li N, Li Q, Ye M, Zheng H, Yu J, Wu H, Sun J, et al. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 2010, 8(11):e1000533. 10.1371/journal.pbio.1000533, 2976721, 21085693.
    • (2010) PLoS Biol , vol.8 , Issue.11
    • Li, Y.1    Zhu, J.2    Tian, G.3    Li, N.4    Li, Q.5    Ye, M.6    Zheng, H.7    Yu, J.8    Wu, H.9    Sun, J.10
  • 16
    • 0026546877 scopus 로고
    • A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
    • 10.1073/pnas.89.5.1827, 48546, 1542678
    • Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A 1992, 89(5):1827-1831. 10.1073/pnas.89.5.1827, 48546, 1542678.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , Issue.5 , pp. 1827-1831
    • Frommer, M.1    McDonald, L.E.2    Millar, D.S.3    Collis, C.M.4    Watt, F.5    Grigg, G.W.6    Molloy, P.L.7    Paul, C.L.8
  • 17
    • 61449426211 scopus 로고    scopus 로고
    • Methylated DNA immunoprecipitation (MeDIP)
    • 10.1007/978-1-59745-522-0_5, 18987806
    • Mohn F, Weber M, Schubeler D, Roloff TC. Methylated DNA immunoprecipitation (MeDIP). Methods Mol Biol 2009, 507:55-64. 10.1007/978-1-59745-522-0_5, 18987806.
    • (2009) Methods Mol Biol , vol.507 , pp. 55-64
    • Mohn, F.1    Weber, M.2    Schubeler, D.3    Roloff, T.C.4
  • 18
    • 77449127799 scopus 로고    scopus 로고
    • MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
    • 10.1093/nar/gkp992, 2811030, 19906696
    • Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 2010, 38(2):391-399. 10.1093/nar/gkp992, 2811030, 19906696.
    • (2010) Nucleic Acids Res , vol.38 , Issue.2 , pp. 391-399
    • Serre, D.1    Lee, B.H.2    Ting, A.H.3
  • 19
    • 77957951913 scopus 로고    scopus 로고
    • Whole-genome DNA methylation profiling using MethylCap-seq
    • 10.1016/j.ymeth.2010.06.012, 20542119
    • Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG. Whole-genome DNA methylation profiling using MethylCap-seq. Methods 2010, 52(3):232-236. 10.1016/j.ymeth.2010.06.012, 20542119.
    • (2010) Methods , vol.52 , Issue.3 , pp. 232-236
    • Brinkman, A.B.1    Simmer, F.2    Ma, K.3    Kaan, A.4    Zhu, J.5    Stunnenberg, H.G.6
  • 20
    • 77955433253 scopus 로고    scopus 로고
    • Whole genome DNA methylation analysis based on high throughput sequencing technology
    • 10.1016/j.ymeth.2010.04.009, 20430099
    • Li N, Ye M, Li Y, Yan Z, Butcher LM, Sun J, Han X, Chen Q, Zhang X, Wang J. Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods 2010, 52(3):203-212. 10.1016/j.ymeth.2010.04.009, 20430099.
    • (2010) Methods , vol.52 , Issue.3 , pp. 203-212
    • Li, N.1    Ye, M.2    Li, Y.3    Yan, Z.4    Butcher, L.M.5    Sun, J.6    Han, X.7    Chen, Q.8    Zhang, X.9    Wang, J.10
  • 21
    • 77957932941 scopus 로고    scopus 로고
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    • 10.1038/nbt.1682, 2955169, 20852635
    • Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010, 28(10):1097-1105. 10.1038/nbt.1682, 2955169, 20852635.
    • (2010) Nat Biotechnol , vol.28 , Issue.10 , pp. 1097-1105
    • Harris, R.A.1    Wang, T.2    Coarfa, C.3    Nagarajan, R.P.4    Hong, C.5    Downey, S.L.6    Johnson, B.E.7    Fouse, S.D.8    Delaney, A.9    Zhao, Y.10
  • 22
    • 79551590211 scopus 로고    scopus 로고
    • W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data
    • 10.1093/bioinformatics/btq669, 3031039, 21138948
    • Lan X, Bonneville R, Apostolos J, Wu W, Jin VX. W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics 2011, 27(3):428-430. 10.1093/bioinformatics/btq669, 3031039, 21138948.
    • (2011) Bioinformatics , vol.27 , Issue.3 , pp. 428-430
    • Lan, X.1    Bonneville, R.2    Apostolos, J.3    Wu, W.4    Jin, V.X.5
  • 24
    • 48249140621 scopus 로고    scopus 로고
    • FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
    • 10.1093/bioinformatics/btn305, 2638869, 18599518
    • Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24(15):1729-1730. 10.1093/bioinformatics/btn305, 2638869, 18599518.
    • (2008) Bioinformatics , vol.24 , Issue.15 , pp. 1729-1730
    • Fejes, A.P.1    Robertson, G.2    Bilenky, M.3    Varhol, R.4    Bainbridge, M.5    Jones, S.J.6
  • 25
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6(11 Suppl):S22-32.
    • (2009) Nat Methods , vol.6 , Issue.11 SUPPL
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 27
    • 79960115813 scopus 로고    scopus 로고
    • High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology
    • 10.1371/journal.pone.0022226, 3136941, 21779396
    • Lan X, Adams C, Landers M, Dudas M, Krissinger D, Marnellos G, Bonneville R, Xu M, Wang J, Huang TH, et al. High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology. PLoS One 2011, 6(7):e22226. 10.1371/journal.pone.0022226, 3136941, 21779396.
    • (2011) PLoS One , vol.6 , Issue.7
    • Lan, X.1    Adams, C.2    Landers, M.3    Dudas, M.4    Krissinger, D.5    Marnellos, G.6    Bonneville, R.7    Xu, M.8    Wang, J.9    Huang, T.H.10
  • 28
    • 0000570382 scopus 로고
    • On Estimating Regression
    • Nadaraya E. On Estimating Regression. Theor Probab Appl 1964, 9:141-142.
    • (1964) Theor Probab Appl , vol.9 , pp. 141-142
    • Nadaraya, E.1
  • 29
    • 0001762424 scopus 로고
    • Smooth regression analysis
    • Watson G. Smooth regression analysis. Shankya Series A 1964, 26:359-372.
    • (1964) Shankya Series A , vol.26 , pp. 359-372
    • Watson, G.1
  • 30
    • 33847730171 scopus 로고    scopus 로고
    • Strictly monotone and smooth nonparametric regression for two or more variables
    • Dette H, Scheder R. Strictly monotone and smooth nonparametric regression for two or more variables. Can J Stat 2006, 34:535-561.
    • (2006) Can J Stat , vol.34 , pp. 535-561
    • Dette, H.1    Scheder, R.2
  • 31
    • 33846090365 scopus 로고    scopus 로고
    • A simple nonparametric estimator of a strictly monotone regression function
    • Dette H, Neumeyer N, Pilz K. A simple nonparametric estimator of a strictly monotone regression function. Bernoulli 2006, 12:469-490.
    • (2006) Bernoulli , vol.12 , pp. 469-490
    • Dette, H.1    Neumeyer, N.2    Pilz, K.3
  • 33
    • 83655163970 scopus 로고    scopus 로고
    • BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data
    • 10.1111/j.1541-0420.2011.01605.x, 3190637, 21517792
    • Ji Y, Xu Y, Zhang Q, Tsui KW, Yuan Y, Norris C, Liang S, Liang H. BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data. Biometrics 2011, 67:1215-1224. 10.1111/j.1541-0420.2011.01605.x, 3190637, 21517792.
    • (2011) Biometrics , vol.67 , pp. 1215-1224
    • Ji, Y.1    Xu, Y.2    Zhang, Q.3    Tsui, K.W.4    Yuan, Y.5    Norris, C.6    Liang, S.7    Liang, H.8
  • 35
    • 78649291183 scopus 로고    scopus 로고
    • Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
    • 10.1101/gr.110114.110, 2945193, 20802089
    • Chavez L, Jozefczuk J, Grimm C, Dietrich J, Timmermann B, Lehrach H, Herwig R, Adjaye J. Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res 2010, 20(10):1441-1450. 10.1101/gr.110114.110, 2945193, 20802089.
    • (2010) Genome Res , vol.20 , Issue.10 , pp. 1441-1450
    • Chavez, L.1    Jozefczuk, J.2    Grimm, C.3    Dietrich, J.4    Timmermann, B.5    Lehrach, H.6    Herwig, R.7    Adjaye, J.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.