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Volumn 15, Issue 2, 2014, Pages

MOABS: Model based analysis of bisulfite sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE;

EID: 84899049695     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-2-r38     Document Type: Article
Times cited : (219)

References (38)
  • 1
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: islands, start sites, gene bodies and beyond
    • 10.1038/nrg3230, 22641018
    • Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012, 13:484-492. 10.1038/nrg3230, 22641018.
    • (2012) Nat Rev Genet , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 4
    • 84869392308 scopus 로고    scopus 로고
    • Mapping recently identified nucleotide variants in the genome and transcriptome
    • 10.1038/nbt.2398, 3537840, 23138310
    • Song CX, Yi C, He C. Mapping recently identified nucleotide variants in the genome and transcriptome. Nat Biotechnol 2012, 30:1107-1116. 10.1038/nbt.2398, 3537840, 23138310.
    • (2012) Nat Biotechnol , vol.30 , pp. 1107-1116
    • Song, C.X.1    Yi, C.2    He, C.3
  • 5
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide DNA methylation analysis
    • 10.1038/nrg2732, 20125086
    • Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010, 11:191-203. 10.1038/nrg2732, 20125086.
    • (2010) Nat Rev Genet , vol.11 , pp. 191-203
    • Laird, P.W.1
  • 6
    • 77249170184 scopus 로고    scopus 로고
    • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    • 10.1038/nrg2719, 3034103, 20142834
    • Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010, 11:204-220. 10.1038/nrg2719, 3034103, 20142834.
    • (2010) Nat Rev Genet , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 9
    • 84861221693 scopus 로고    scopus 로고
    • Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution
    • 10.1126/science.1220671, 22539555
    • Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S. Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution. Science 2012, 336:934-937. 10.1126/science.1220671, 22539555.
    • (2012) Science , vol.336 , pp. 934-937
    • Booth, M.J.1    Branco, M.R.2    Ficz, G.3    Oxley, D.4    Krueger, F.5    Reik, W.6    Balasubramanian, S.7
  • 12
    • 84871688621 scopus 로고    scopus 로고
    • Analysing and interpreting DNA methylation data
    • 10.1038/nrg3273, 22986265
    • Bock C. Analysing and interpreting DNA methylation data. Nat Rev Genet 2012, 13:705-719. 10.1038/nrg3273, 22986265.
    • (2012) Nat Rev Genet , vol.13 , pp. 705-719
    • Bock, C.1
  • 13
    • 84866853818 scopus 로고    scopus 로고
    • BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
    • 10.1186/gb-2012-13-10-r83, 3491411, 23034175
    • Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol 2012, 13:R83. 10.1186/gb-2012-13-10-r83, 3491411, 23034175.
    • (2012) Genome Biol , vol.13
    • Hansen, K.D.1    Langmead, B.2    Irizarry, R.A.3
  • 14
    • 84866860221 scopus 로고    scopus 로고
    • MethylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
    • 10.1186/gb-2012-13-10-r87, 3491415, 23034086
    • Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 2012, 13:R87. 10.1186/gb-2012-13-10-r87, 3491415, 23034086.
    • (2012) Genome Biol , vol.13
    • Akalin, A.1    Kormaksson, M.2    Li, S.3    Garrett-Bakelman, F.E.4    Figueroa, M.E.5    Melnick, A.6    Mason, C.E.7
  • 15
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: whole genome bisulfite sequence MAPping program
    • Xi Y, Li W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinforma 2009, 10:232.
    • (2009) BMC Bioinforma , vol.10 , pp. 232
    • Xi, Y.1    Li, W.2
  • 18
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
    • 10.1016/j.cell.2011.11.013, 3243364, 22153082
    • Rhee Ho S, Pugh BF. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell 2011, 147:1408-1419. 10.1016/j.cell.2011.11.013, 3243364, 22153082.
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee Ho, S.1    Pugh, B.F.2
  • 19
    • 84868017347 scopus 로고    scopus 로고
    • GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data
    • 10.1093/bioinformatics/bts515, 22923299
    • Feng J, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics 2012, 28:2782-2788. 10.1093/bioinformatics/bts515, 22923299.
    • (2012) Bioinformatics , vol.28 , pp. 2782-2788
    • Feng, J.1    Meyer, C.A.2    Wang, Q.3    Liu, J.S.4    Liu, X.S.5    Zhang, Y.6
  • 20
    • 76549135113 scopus 로고    scopus 로고
    • Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease
    • 10.1073/pnas.0906183107, 2868296, 20080672
    • Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci USA 2010, 107:1757-1764. 10.1073/pnas.0906183107, 2868296, 20080672.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 1757-1764
    • Feinberg, A.P.1    Irizarry, R.A.2
  • 22
    • 84899104830 scopus 로고    scopus 로고
    • Comparison of exact confidence intervals for the difference between two independent binomial proportions
    • Kawasaki Y. Comparison of exact confidence intervals for the difference between two independent binomial proportions. Adv Appl Stat 2010, 15:157-170.
    • (2010) Adv Appl Stat , vol.15 , pp. 157-170
    • Kawasaki, Y.1
  • 23
    • 0000692018 scopus 로고
    • Exact confidence limits for binomial proportions-Pearson and Hartley revisited
    • Brenner DJ, Quan H. Exact confidence limits for binomial proportions-Pearson and Hartley revisited. J R Stat Soc. Series D (The Statistician) 1990, 39:391-397.
    • (1990) J R Stat Soc. Series D (The Statistician) , vol.39 , pp. 391-397
    • Brenner, D.J.1    Quan, H.2
  • 24
    • 84899050224 scopus 로고    scopus 로고
    • BSeQC: quality control of bisulfite sequencing experiments
    • 10.1093/bioinformatics/btt548, 24064417
    • Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W. BSeQC: quality control of bisulfite sequencing experiments. Bioinformatics 2013, 29:3227-3229. 10.1093/bioinformatics/btt548, 24064417.
    • (2013) Bioinformatics , vol.29 , pp. 3227-3229
    • Lin, X.1    Sun, D.2    Rodriguez, B.3    Zhao, Q.4    Sun, H.5    Zhang, Y.6    Li, W.7
  • 25
    • 84857331867 scopus 로고    scopus 로고
    • Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome
    • 10.1016/j.cell.2011.12.035, 3343639, 22341451
    • Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL, Ren B. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 2012, 148:816-831. 10.1016/j.cell.2011.12.035, 3343639, 22341451.
    • (2012) Cell , vol.148 , pp. 816-831
    • Xie, W.1    Barr, C.L.2    Kim, A.3    Yue, F.4    Lee, A.Y.5    Eubanks, J.6    Dempster, E.L.7    Ren, B.8
  • 28
    • 79955137160 scopus 로고    scopus 로고
    • A compendium of genome-wide hematopoietic transcription factor maps supports the identification of gene regulatory control mechanisms
    • 10.1016/j.exphem.2011.02.009, 21338655
    • Hannah R, Joshi A, Wilson NK, Kinston S, Gottgens B. A compendium of genome-wide hematopoietic transcription factor maps supports the identification of gene regulatory control mechanisms. Exp Hematol 2011, 39:531-541. 10.1016/j.exphem.2011.02.009, 21338655.
    • (2011) Exp Hematol , vol.39 , pp. 531-541
    • Hannah, R.1    Joshi, A.2    Wilson, N.K.3    Kinston, S.4    Gottgens, B.5
  • 31
    • 79956323623 scopus 로고    scopus 로고
    • Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation
    • 10.1038/nature10008, 21460836
    • Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 2011, 473:398-402. 10.1038/nature10008, 21460836.
    • (2011) Nature , vol.473 , pp. 398-402
    • Ficz, G.1    Branco, M.R.2    Seisenberger, S.3    Santos, F.4    Krueger, F.5    Hore, T.A.6    Marques, C.J.7    Andrews, S.8    Reik, W.9
  • 32
    • 84886811866 scopus 로고    scopus 로고
    • Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
    • Min Zhao QW, Quan W, Peilin J, Zhongming Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinforma 2013, 14:S1.
    • (2013) BMC Bioinforma , vol.14
    • Min Zhao, Q.W.1    Quan, W.2    Peilin, J.3    Zhongming, Z.4
  • 33
    • 0032580377 scopus 로고    scopus 로고
    • Interval estimation for the difference between independent proportions: comparison of eleven methods
    • 10.1002/(SICI)1097-0258(19980430)17:8<873::AID-SIM779>3.0.CO;2-I, 9595617
    • Newcombe RG. Interval estimation for the difference between independent proportions: comparison of eleven methods. Stat Med 1998, 17:873-890. 10.1002/(SICI)1097-0258(19980430)17:8<873::AID-SIM779>3.0.CO;2-I, 9595617.
    • (1998) Stat Med , vol.17 , pp. 873-890
    • Newcombe, R.G.1
  • 34
    • 84946650481 scopus 로고
    • Probable inference, the law of succession, and statistical inference
    • Wilson EB. Probable inference, the law of succession, and statistical inference. J Am Stat Assoc 1927, 22:209-212.
    • (1927) J Am Stat Assoc , vol.22 , pp. 209-212
    • Wilson, E.B.1
  • 35
    • 34547165115 scopus 로고    scopus 로고
    • Small-sample comparisons of confidence intervals for the difference of two independent binomial proportions
    • Santner TJ, Pradhan V, Senchaudhuri P, Mehta CR, Tamhane A. Small-sample comparisons of confidence intervals for the difference of two independent binomial proportions. Comput Stat Data Anal 2007, 51:5791-5799.
    • (2007) Comput Stat Data Anal , vol.51 , pp. 5791-5799
    • Santner, T.J.1    Pradhan, V.2    Senchaudhuri, P.3    Mehta, C.R.4    Tamhane, A.5
  • 36
    • 84899111928 scopus 로고    scopus 로고
    • Score intervals for the difference of two binomial proportions
    • Nurminen MM, Newcombe RG. Score intervals for the difference of two binomial proportions. http://markstat.net/en/images/stories/notes_on_score_intervals.pdf.
    • Nurminen, M.M.1    Newcombe, R.G.2
  • 37
    • 41049086885 scopus 로고    scopus 로고
    • Confidence interval of the difference of two independent binomial proportions using weighted profile likelihood
    • Tathagata
    • Pradhan VB, Tathagata. Confidence interval of the difference of two independent binomial proportions using weighted profile likelihood. Commun Stat Simul Comput 2008, 37:645-659.
    • (2008) Commun Stat Simul Comput , vol.37 , pp. 645-659
    • Pradhan, V.B.1
  • 38
    • 0001277701 scopus 로고
    • Small sample confidence intervals for the difference,ratio and odds ratio of two success probabilities
    • Coe PR, Tamhane AC. Small sample confidence intervals for the difference,ratio and odds ratio of two success probabilities. Commun Stat Simul Comput 1993, 22:925-938.
    • (1993) Commun Stat Simul Comput , vol.22 , pp. 925-938
    • Coe, P.R.1    Tamhane, A.C.2


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