메뉴 건너뛰기




Volumn 30, Issue 13, 2014, Pages 1814-1822

DMAP: Differential methylation analysis package for RRBS and WGBS data

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER PROGRAM; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES;

EID: 84903709420     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu126     Document Type: Article
Times cited : (111)

References (35)
  • 1
    • 84866860221 scopus 로고    scopus 로고
    • Methylkit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles
    • Akalin, A. et al. (2012a) methylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol., 13, R87
    • (2012) Genome Biol , vol.13
    • Akalin, A.1
  • 2
    • 84864031521 scopus 로고    scopus 로고
    • Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia
    • Akalin, A. et al. (2012b) Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet., 8, e1002781
    • (2012) PLoS Genet , vol.8
    • Akalin, A.1
  • 3
    • 77951836633 scopus 로고    scopus 로고
    • Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis
    • Baranzini, S.E. et al. (2010) Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature, 464, 1351-1356
    • (2010) Nature , vol.464 , pp. 1351-1356
    • Baranzini, S.E.1
  • 4
    • 0036561649 scopus 로고    scopus 로고
    • Altered methylation patterns in cancer cell genomes: Cause or consequencë
    • Baylin, S. and Bestor, T.H. (2002) Altered methylation patterns in cancer cell genomes: Cause or consequencë. Cancer Cell, 1, 299-305
    • (2002) Cancer Cell , vol.1 , pp. 299-305
    • Baylin, S.1    Bestor, T.H.2
  • 5
    • 77957937011 scopus 로고    scopus 로고
    • Quantitative comparison of genome-wide DNA methylation mapping technologies
    • Bock, C. et al. (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol., 28, 1106-1114
    • (2010) Nat. Biotechnol , vol.28 , pp. 1106-1114
    • Bock, C.1
  • 6
    • 79551677421 scopus 로고    scopus 로고
    • Reference Maps of human ES and iPS cell variation enable high-Throughput characterization of pluripotent cell lines
    • Bock, C. et al. (2011) Reference Maps of human ES and iPS cell variation enable high-Throughput characterization of pluripotent cell lines. Cell, 144, 439-452
    • (2011) Cell , vol.144 , pp. 439-452
    • Bock, C.1
  • 7
    • 84865369147 scopus 로고    scopus 로고
    • DNA methylation Dynamics during in vivo differentiation of blood and skin stem cells
    • Bock, C. et al. (2012) DNA methylation Dynamics during in vivo differentiation of blood and skin stem cells. Mol. Cell, 47, 633-647
    • (2012) Mol. Cell , vol.47 , pp. 633-647
    • Bock, C.1
  • 8
    • 84872573541 scopus 로고    scopus 로고
    • PASS-bis: A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads
    • Campagna, D. et al. (2013) PASS-bis: A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. Bioinformatics, 29, 268-270
    • (2013) Bioinformatics , vol.29 , pp. 268-270
    • Campagna, D.1
  • 9
    • 84869013266 scopus 로고    scopus 로고
    • Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries
    • Chatterjee, A. et al. (2012) Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries. J. Biomed. Biotechnol., 2012, 741542
    • (2012) J. Biomed. Biotechnol , vol.2012 , pp. 741542
    • Chatterjee, A.1
  • 10
    • 84861563688 scopus 로고    scopus 로고
    • Comparison of alignment software for genome-wide bisulphite sequence data
    • Chatterjee, A. et al. (2012) Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Res., 40, e79
    • (2012) Nucleic Acids Res , vol.40
    • Chatterjee, A.1
  • 11
    • 84883524651 scopus 로고    scopus 로고
    • Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing
    • Chatterjee, A. et al. (2013) Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. Epigenetics, 8, 979-989
    • (2013) Epigenetics , vol.8 , pp. 979-989
    • Chatterjee, A.1
  • 12
    • 77951125407 scopus 로고    scopus 로고
    • BS Seeker: Precise mapping for bisulfite sequencing
    • Chen, P.Y. et al. (2010) BS Seeker: Precise mapping for bisulfite sequencing. BMC Bioinformatics, 11, 203
    • (2010) BMC Bioinformatics , vol.11 , pp. 203
    • Chen, P.Y.1
  • 13
    • 84885001955 scopus 로고    scopus 로고
    • DNA methylation and differentiation: Silencing, upregulation and modulation of gene expression
    • Ehrlich, M. and Lacey, M. (2013) DNA methylation and differentiation: Silencing, upregulation and modulation of gene expression. Epigenomics, 5, 553-568
    • (2013) Epigenomics , vol.5 , pp. 553-568
    • Ehrlich, M.1    Lacey, M.2
  • 14
    • 80052306947 scopus 로고    scopus 로고
    • Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
    • Gertz, J. et al. (2011) Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet., 7, e1002228
    • (2011) PLoS Genet , vol.7
    • Gertz, J.1
  • 15
    • 84874650026 scopus 로고    scopus 로고
    • Evidence of a conserved functional role for DNA methylation in termites
    • Glastad, K.M. et al. (2013) Evidence of a conserved functional role for DNA methylation in termites. Insect Mol. Biol., 22, 143-154
    • (2013) Insect Mol. Biol , vol.22 , pp. 143-154
    • Glastad, K.M.1
  • 16
    • 77449153454 scopus 로고    scopus 로고
    • Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
    • Gu, H. et al. (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods, 7, 133-136
    • (2010) Nat. Methods , vol.7 , pp. 133-136
    • Gu, H.1
  • 17
    • 84866853818 scopus 로고    scopus 로고
    • BSmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
    • Hansen, K.D. et al. (2012) BSmooth: From whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol., 13, R83
    • (2012) Genome Biol , vol.13
    • Hansen, K.D.1
  • 18
    • 84879895082 scopus 로고    scopus 로고
    • Detection of significantly differentially methylated regions in targeted bisulfite sequencing data
    • Hebestreit, K. et al. (2013) Detection of significantly differentially methylated regions in targeted bisulfite sequencing data. Bioinformatics, 29, 1647-1653
    • (2013) Bioinformatics , vol.29 , pp. 1647-1653
    • Hebestreit, K.1
  • 19
    • 84876042374 scopus 로고    scopus 로고
    • In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
    • Ivanov, M. et al. (2013) In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes. Nucleic Acids Res., 41, e72
    • (2013) Nucleic Acids Res , vol.41
    • Ivanov, M.1
  • 20
    • 58149181382 scopus 로고    scopus 로고
    • Transterm: A database to aid the analysis of regulatory sequences in mRNAs
    • Jacobs, G.H. et al. (2009) Transterm: A database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Res., 37, D72-D76
    • (2009) Nucleic Acids Res , vol.37
    • Jacobs, G.H.1
  • 21
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
    • Krueger, F. and Andrews, S.R. (2011) Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572
    • (2011) Bioinformatics , vol.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 22
    • 84898950243 scopus 로고    scopus 로고
    • Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
    • Epub ahead of print, doi:10.1093/nar/gkt1325, January 3 2014
    • Kunde-Ramamoorthy, G. et al. (2014) Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Res. [Epub ahead of print, doi:10.1093/nar/gkt1325, January 3, 2014].
    • (2014) Nucleic Acids Res. [
    • Kunde-Ramamoorthy, G.1
  • 23
    • 77249170184 scopus 로고    scopus 로고
    • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    • Law, J.A. and Jacobsen, S.E. (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet., 11, 204-220
    • (2010) Nat. Rev. Genet , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 24
    • 78649969065 scopus 로고    scopus 로고
    • The DNA methylome of human peripheral blood mononuclear cells
    • Li, Y. et al. (2010) The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol., 8, e1000533
    • (2010) PLoS Biol , vol.8
    • Li, Y.1
  • 25
    • 84866860274 scopus 로고    scopus 로고
    • BatMeth: Improved mapper for bisulfite sequencing reads on DNA methylation
    • Lim, J.Q. et al. (2012) BatMeth: Improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol., 13, R82
    • (2012) Genome Biol , vol.13
    • Lim, J.Q.1
  • 27
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • Schmieder, R. and Edwards, R. (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863-864
    • (2011) Bioinformatics , vol.27 , pp. 863-864
    • Schmieder, R.1    Edwards, R.2
  • 28
    • 79960926264 scopus 로고    scopus 로고
    • Dynamic CpG island methylation landscape in oocytes and preimplantation embryos
    • Smallwood, S.A. et al. (2011) Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat. Genet., 43, 811-814
    • (2011) Nat. Genet , vol.43 , pp. 811-814
    • Smallwood, S.A.1
  • 29
    • 70350697851 scopus 로고    scopus 로고
    • Updates to the RMAP short-read mapping software
    • Smith, A.D. et al. (2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25, 2841-2842
    • (2009) Bioinformatics , vol.25 , pp. 2841-2842
    • Smith, A.D.1
  • 30
    • 79955510962 scopus 로고    scopus 로고
    • Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer
    • Steine, E.J. et al. (2011) Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer. J. Clin. Invest., 121, 1748-1752
    • (2011) J. Clin. Invest , vol.121 , pp. 1748-1752
    • Steine, E.J.1
  • 31
    • 84882504928 scopus 로고    scopus 로고
    • MethyQA: A pipeline for bisulfite-Treated methylation sequencing quality assessment
    • Sun, S. et al. (2013) MethyQA: A pipeline for bisulfite-Treated methylation sequencing quality assessment. BMC Bioinformatics, 14, 259
    • (2013) BMC Bioinformatics , vol.14 , pp. 259
    • Sun, S.1
  • 32
    • 84875634162 scopus 로고    scopus 로고
    • Integrative genomics viewer (igv): High-performance genomics data visualization and exploration
    • Thorvaldsdottir, H. et al. (2013) Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief. Bioinform, 14, 178-192
    • (2013) Brief. Bioinform , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1
  • 33
    • 78651434680 scopus 로고    scopus 로고
    • Slim: A sliding linear model for estimating the proportion of true null hypotheses in Datasets with dependence structures
    • Wang, H.Q. et al. (2011) SLIM: A sliding linear model for estimating the proportion of true null hypotheses in Datasets with dependence structures. Bioinformatics, 27, 225-231
    • (2011) Bioinformatics , vol.27 , pp. 225-231
    • Wang, H.Q.1
  • 34
    • 84856568045 scopus 로고    scopus 로고
    • Rrbsmap: A fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
    • Xi, Y. et al. (2012) RRBSMAP: A fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics, 28, 430-432
    • (2012) Bioinformatics , vol.28 , pp. 430-432
    • Xi, Y.1
  • 35
    • 84882884517 scopus 로고    scopus 로고
    • Charting a dynamic dna methylation landscape of the human genome
    • Ziller, M.J. et al. (2013) Charting a dynamic DNA methylation landscape of the human genome. Nature, 500, 477-481.
    • (2013) Nature , vol.500 , pp. 477-481
    • Ziller, M.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.