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Volumn 41, Issue 11, 2013, Pages 8335-8336

Erratum: COHCAP: An integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis (Nucleic Acids Research (2013) 41: 11 (e117) DOI: 10.1093/nar/gkt242);COHCAP: An integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis

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ESTROGEN RECEPTOR ALPHA;

EID: 84878866495     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkz663     Document Type: Erratum
Times cited : (99)

References (64)
  • 2
    • 33748055105 scopus 로고    scopus 로고
    • MIRA-assisted microarray analysis, a new technology for the determination of dna methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells
    • Rauch, T., Li, H., Wu, X. and Pfeifer, G.P. (2006) MIRA-assisted microarray analysis, a new technology for the determination of dna methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res., 66, 7939-7947.
    • (2006) Cancer Res , vol.66 , pp. 7939-7947
    • Rauch, T.1    Li, H.2    Wu, X.3    Pfeifer, G.P.4
  • 3
    • 84871688621 scopus 로고    scopus 로고
    • Analysing and interpreting DNA methylation data
    • Bock, C. (2012) Analysing and interpreting DNA methylation data. Nat. Rev. Genet., 13, 705-719.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 705-719
    • Bock, C.1
  • 4
    • 84871194526 scopus 로고    scopus 로고
    • Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale
    • Barrera, V. and Peinado, M.A. (2012) Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale. Nucleic Acids Res., 40, 11490-11498.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 11490-11498
    • Barrera, V.1    Peinado, M.A.2
  • 5
    • 84862157386 scopus 로고    scopus 로고
    • Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc
    • Roessler, J., Ammerpohl, O., Gutwein, J., Hasemeier, B., Anwar, S., Kreipe, H. and Lehmann, U. (2012) Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc. BMC Res. Notes, 5, 210.
    • (2012) BMC Res. Notes , vol.5 , pp. 210
    • Roessler, J.1    Ammerpohl, O.2    Gutwein, J.3    Hasemeier, B.4    Anwar, S.5    Kreipe, H.6    Lehmann, U.7
  • 8
    • 79959838081 scopus 로고    scopus 로고
    • Integrated genomic analyses of ovarian carcinoma
    • The Cancer Genome Atlas Network
    • The Cancer Genome Atlas Network. (2011) Integrated genomic analyses of ovarian carcinoma. Nature, 474, 609-615.
    • (2011) Nature , vol.474 , pp. 609-615
  • 9
    • 84863922124 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of human colon and rectal cancer
    • The Cancer Genome Atlas Network
    • The Cancer Genome Atlas Network. (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487, 330-337.
    • (2012) Nature , vol.487 , pp. 330-337
  • 10
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • The Cancer Genome Atlas Network
    • The Cancer Genome Atlas Network. (2012) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
    • (2012) Nature , vol.490 , pp. 61-70
  • 11
    • 84866894408 scopus 로고    scopus 로고
    • Comprehensive genomic characterization of squamous cell lung cancers
    • The Cancer Genome Atlas Network
    • The Cancer Genome Atlas Network. (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature, 489, 519-525.
    • (2012) Nature , vol.489 , pp. 519-525
  • 15
    • 84873476594 scopus 로고    scopus 로고
    • Epigenome-wide association study in the European Prospective Investigation into cancer and nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking
    • Shenker, N.S., Polidoro, S., van Veldhoven, K., Sacerdote, C., Ricceri, F., Birrell, M.A., Belvisi, M.G., Brown, R., Vineis, P. and Flanagan, J.M. (2013) Epigenome-wide association study in the European Prospective Investigation into cancer and nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking. Hum. Mol. Genet., 22, 843-851.
    • (2013) Hum. Mol. Genet. , vol.22 , pp. 843-851
    • Shenker, N.S.1    Polidoro, S.2    Van Veldhoven, K.3    Sacerdote, C.4    Ricceri, F.5    Birrell, M.A.6    Belvisi, M.G.7    Brown, R.8    Vineis, P.9    Flanagan, J.M.10
  • 21
    • 84867159872 scopus 로고    scopus 로고
    • Measuring the methylome in clinical samples: Improved processing of the infinium human methylation450 beadchip array
    • Pan, H., Chen, L., Dogra, S., Ling Teh, A., Tan, J.H., Lim, Y.I., Lim, Y.C., Jin, S., Lee, Y.K., Ng, P.Y. et al. (2012) Measuring the methylome in clinical samples: improved processing of the infinium human methylation450 beadchip array. Epigenetics, 7, 1173-1187.
    • (2012) Epigenetics , vol.7 , pp. 1173-1187
    • Pan, H.1    Chen, L.2    Dogra, S.3    Ling Teh, A.4    Tan, J.H.5    Lim, Y.I.6    Lim, Y.C.7    Jin, S.8    Lee, Y.K.9    Ng, P.Y.10
  • 23
    • 84871197314 scopus 로고    scopus 로고
    • A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network
    • Lee, S.T., Xiao, Y., Muench, M.O., Xiao, J., Fomin, M.E., Wiencke, J.K., Zheng, S., Dou, X., de Smith, A., Chokkalingam, A. et al. (2012) A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res., 40, 11339-11351.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 11339-11351
    • Lee, S.T.1    Xiao, Y.2    Muench, M.O.3    Xiao, J.4    Fomin, M.E.5    Wiencke, J.K.6    Zheng, S.7    Dou, X.8    De Smith, A.9    Chokkalingam, A.10
  • 25
    • 84863291989 scopus 로고    scopus 로고
    • MethLAB: A graphical user interface package for the analysis of array-based DNA methylation data
    • Kilaru, V., Barfield, R.T., Schroeder, J.W., Smith, A.K. and Conneely, K.N. (2012) MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data. Epigenetics, 7, 225-229.
    • (2012) Epigenetics , vol.7 , pp. 225-229
    • Kilaru, V.1    Barfield, R.T.2    Schroeder, J.W.3    Smith, A.K.4    Conneely, K.N.5
  • 26
    • 84876066517 scopus 로고    scopus 로고
    • Identification of DNA methylation biomarkers from Infinium arrays
    • Emes, R.D. and Wessely, F. (2012) Identification of DNA methylation biomarkers from Infinium arrays. Front. Genet., 3, 161.
    • (2012) Front. Genet. , vol.3 , pp. 161
    • Emes, R.D.1    Wessely, F.2
  • 27
    • 84860492186 scopus 로고    scopus 로고
    • CpGassoc: An R function for analysis of DNA methylation microarray data
    • Barfield, R.T., Kilaru, V., Smith, A.K. and Conneely, K.N. (2012) CpGassoc: an R function for analysis of DNA methylation microarray data. Bioinformatics, 28, 1280-1281.
    • (2012) Bioinformatics , vol.28 , pp. 1280-1281
    • Barfield, R.T.1    Kilaru, V.2    Smith, A.K.3    Conneely, K.N.4
  • 28
    • 84861135864 scopus 로고    scopus 로고
    • Penalized logistic regression for highdimensional DNA methylation data with case-control studies
    • Sun, H. and Wang, S. (2012) Penalized logistic regression for highdimensional DNA methylation data with case-control studies. Bioinformatics, 28, 1368-1375.
    • (2012) Bioinformatics , vol.28 , pp. 1368-1375
    • Sun, H.1    Wang, S.2
  • 29
    • 84875376002 scopus 로고    scopus 로고
    • MENT: Methylation and expression database of normal and tumor tissues
    • Baek, S.J., Yang, S., Kang, T.W., Park, S.M., Kim, Y.S. and Kim, S.Y. (2013) MENT: methylation and expression database of normal and tumor tissues. Gene, 518, 194-200.
    • (2013) Gene , vol.518 , pp. 194-200
    • Baek, S.J.1    Yang, S.2    Kang, T.W.3    Park, S.M.4    Kim, Y.S.5    Kim, S.Y.6
  • 33
    • 84859910536 scopus 로고    scopus 로고
    • A unique regulatory phase of DNA methylation in the early mammalian embryo
    • Smith, Z.D., Chan, M.M., Mikkelsen, T.S., Gu, H., Gnirke, A., Regev, A. and Meissner, A. (2012) A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature, 484, 339-344.
    • (2012) Nature , vol.484 , pp. 339-344
    • Smith, Z.D.1    Chan, M.M.2    Mikkelsen, T.S.3    Gu, H.4    Gnirke, A.5    Regev, A.6    Meissner, A.7
  • 34
    • 84866853818 scopus 로고    scopus 로고
    • BSmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
    • Hansen, K., Langmead, B. and Irizarry, R. (2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol., 13, R83.
    • (2012) Genome Biol. , vol.13
    • Hansen, K.1    Langmead, B.2    Irizarry, R.3
  • 37
    • 84862173149 scopus 로고    scopus 로고
    • SWAN: Subsetquantile within array normalization for illumina infinium humanmethylation450 beadchips
    • Maksimovic, J., Gordon, L. and Oshlack, A. (2012) SWAN: Subsetquantile within array normalization for illumina infinium humanmethylation450 beadchips. Genome Biol., 13, R44.
    • (2012) Genome Biol. , vol.13
    • Maksimovic, J.1    Gordon, L.2    Oshlack, A.3
  • 38
    • 84862266444 scopus 로고    scopus 로고
    • Complete pipeline for Infinium-Human methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation
    • Touleimat, N. and Tost, J. (2012) Complete pipeline for Infinium-Human methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics, 4, 325-341.
    • (2012) Epigenomics , vol.4 , pp. 325-341
    • Touleimat, N.1    Tost, J.2
  • 39
    • 84872564830 scopus 로고    scopus 로고
    • A Beta-Mixture Quantile Normalisation method for correcting probe design bias in illumina infinium 450k DNA methylation data
    • Teschendorff, A.E., Marabita, F., Lechner, M., Bartlett, T., Tegner, J., Gomez-Cabrero, D. and Beck, S. (2012) A Beta-Mixture Quantile Normalisation method for correcting probe design bias in illumina infinium 450k DNA methylation data. Bioinformatics, 29, 189-196.
    • (2012) Bioinformatics , vol.29 , pp. 189-196
    • Teschendorff, A.E.1    Marabita, F.2    Lechner, M.3    Bartlett, T.4    Tegner, J.5    Gomez-Cabrero, D.6    Beck, S.7
  • 40
    • 46249088370 scopus 로고    scopus 로고
    • Lumi: A pipeline for processing illumina microarray
    • Du, P., Kibbe, W.A. and Lin, S.M. (2008) lumi: a pipeline for processing illumina microarray. Bioinformatics, 24, 1547-1548.
    • (2008) Bioinformatics , vol.24 , pp. 1547-1548
    • Du, P.1    Kibbe, W.A.2    Lin, S.M.3
  • 41
    • 79957851822 scopus 로고    scopus 로고
    • Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies
    • Teschendorff, A.E., Zhuang, J. and Widschwendter, M. (2011) Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. Bioinformatics, 27, 1496-1505.
    • (2011) Bioinformatics , vol.27 , pp. 1496-1505
    • Teschendorff, A.E.1    Zhuang, J.2    Widschwendter, M.3
  • 42
    • 57749084635 scopus 로고    scopus 로고
    • A general framework for multiple testing dependence
    • Leek, J.T. and Storey, J.D. (2008) A general framework for multiple testing dependence. Proc. Natl Acad. Sci. USA, 105, 18718-18723.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 18718-18723
    • Leek, J.T.1    Storey, J.D.2
  • 43
    • 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
  • 45
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol, 57, 289-300.
    • (1995) J R Stat Soc Series B Stat Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 51
    • 84870525593 scopus 로고    scopus 로고
    • A Comparison of the whole genome approach of MeDIP-Seq to the targeted approach of the infinium humanmethylation450 BeadChip(-) for methylome profiling
    • Clark, C., Palta, P., Joyce, C.J., Scott, C., Grundberg, E., Deloukas, P., Palotie, A. and Coffey, A.J. (2012) A Comparison of the whole genome approach of MeDIP-Seq to the targeted approach of the infinium humanmethylation450 BeadChip(-) for methylome profiling. PLoS One, 7, e50233.
    • (2012) PLoS One , vol.7
    • Clark, C.1    Palta, P.2    Joyce, C.J.3    Scott, C.4    Grundberg, E.5    Deloukas, P.6    Palotie, A.7    Coffey, A.J.8
  • 57
    • 80055027583 scopus 로고    scopus 로고
    • Protective effects of white button mushroom (Agaricus bisporus) against hepatic steatosis in ovariectomized mice as a model of postmenopausal women
    • Kanaya, N., Kubo, M., Liu, Z., Chu, P., Wang, C., Yuan, Y.C. and Chen, Y. (2011) Protective effects of white button mushroom (Agaricus bisporus) against hepatic steatosis in ovariectomized mice as a model of postmenopausal women. PLoS One, 6, e26654.
    • (2011) PLoS One , vol.6
    • Kanaya, N.1    Kubo, M.2    Liu, Z.3    Chu, P.4    Wang, C.5    Yuan, Y.C.6    Chen, Y.7
  • 61
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J., Nekrutenko, A., Taylor, J. and Team, T.G. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
    • (2010) Genome Biol. , vol.11
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3    Team, T.G.4
  • 63
    • 84867400649 scopus 로고    scopus 로고
    • DNA methylation based biomarkers: Practical considerations and applications
    • How Kit, A., Nielsen, H.M. and Tost, J. (2012) DNA methylation based biomarkers: Practical considerations and applications. Biochimie, 94, 2314-2337.
    • (2012) Biochimie , vol.94 , pp. 2314-2337
    • How Kit, A.1    Nielsen, H.M.2    Tost, J.3
  • 64
    • 84870322656 scopus 로고    scopus 로고
    • Genome-wide methylation screen in lowgrade breast cancer identifies novel epigenetically altered genes as potential biomarkers for tumor diagnosis
    • Faryna, M., Konermann, C., Aulmann, S., Bermejo, J.L., Brugger, M., Diederichs, S., Rom, J., Weichenhan, D., Claus, R., Rehli, M. et al. (2012) Genome-wide methylation screen in lowgrade breast cancer identifies novel epigenetically altered genes as potential biomarkers for tumor diagnosis. FASEB J., 26, 4937-4950.
    • (2012) FASEB J. , vol.26 , pp. 4937-4950
    • Faryna, M.1    Konermann, C.2    Aulmann, S.3    Bermejo, J.L.4    Brugger, M.5    Diederichs, S.6    Rom, J.7    Weichenhan, D.8    Claus, R.9    Rehli, M.10


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