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Volumn 18, Issue 1, 2017, Pages

Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome (Genome Biology (2017) 18 (50) DOI: 10.1186/s13059-017-1173-7);Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

(33)  Cheung, Warren A a   Shao, Xiaojian a   Morin, Andréanne a   Siroux, Valérie b   Kwan, Tony a   Ge, Bing a   Aïssi, Dylan b   Chen, Lu c,d   Vasquez, Louella c   Allum, Fiona a   Guénard, Frédéric e   Bouzigon, Emmanuelle f   Simon, Marie Michelle a   Boulier, Elodie a   Redensek, Adriana a   Watt, Stephen c   Datta, Avik g   Clarke, Laura g   Flicek, Paul g   Mead, Daniel c   more..

f INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; HISTONE;

EID: 85014936699     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-019-1702-7     Document Type: Erratum
Times cited : (64)

References (56)
  • 7
    • 84890172667 scopus 로고    scopus 로고
    • Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements
    • Grundberg E, Meduri E, Sandling JK, Hedman AK, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, et al. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet. 2013;93:876-90.
    • (2013) Am J Hum Genet , vol.93 , pp. 876-890
    • Grundberg, E.1    Meduri, E.2    Sandling, J.K.3    Hedman, A.K.4    Keildson, S.5    Buil, A.6    Busche, S.7    Yuan, W.8    Nisbet, J.9    Sekowska, M.10
  • 8
    • 84897489039 scopus 로고    scopus 로고
    • The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts
    • Wagner JR, Busche S, Ge B, Kwan T, Pastinen T, Blanchette M. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol. 2014;15:R37.
    • (2014) Genome Biol , vol.15 , pp. R37
    • Wagner, J.R.1    Busche, S.2    Ge, B.3    Kwan, T.4    Pastinen, T.5    Blanchette, M.6
  • 9
    • 84908214376 scopus 로고    scopus 로고
    • Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping
    • Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T. Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping. Epigenetics. 2014;9:1238-51.
    • (2014) Epigenetics , vol.9 , pp. 1238-1251
    • Light, N.1    Adoue, V.2    Ge, B.3    Chen, S.H.4    Kwan, T.5    Pastinen, T.6
  • 11
    • 77954238686 scopus 로고    scopus 로고
    • Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
    • Shoemaker R, Deng J, Wang W, Zhang K. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res. 2010;20:883-9.
    • (2010) Genome Res , vol.20 , pp. 883-889
    • Shoemaker, R.1    Deng, J.2    Wang, W.3    Zhang, K.4
  • 14
    • 78651276230 scopus 로고    scopus 로고
    • Allele-specific DNA, methylation: beyond imprinting
    • Tycko B. Allele-specific DNA, methylation: beyond imprinting. Hum Mol Genet. 2010;19:R210-20.
    • (2010) Hum Mol Genet , vol.19 , pp. R210-R220
    • Tycko, B.1
  • 20
    • 84992176761 scopus 로고    scopus 로고
    • Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells
    • Morin A, Kwan T, Ge B, Letourneau L, Ban M, Tandre K, Caron M, Sandling JK, Carlsson J, Bourque G, et al. Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells. BMC Med Genomics. 2016;9:59.
    • (2016) BMC Med Genomics , vol.9 , pp. 59
    • Morin, A.1    Kwan, T.2    Ge, B.3    Letourneau, L.4    Ban, M.5    Tandre, K.6    Caron, M.7    Sandling, J.K.8    Carlsson, J.9    Bourque, G.10
  • 23
    • 33750078697 scopus 로고    scopus 로고
    • Allelic gene regulation of Pcdh-alpha and Pcdh-gamma clusters involving both monoallelic and biallelic expression in single Purkinje cells
    • Kaneko R, Kato H, Kawamura Y, Esumi S, Hirayama T, Hirabayashi T, Yagi T. Allelic gene regulation of Pcdh-alpha and Pcdh-gamma clusters involving both monoallelic and biallelic expression in single Purkinje cells. J Biol Chem. 2006;281:30551-60.
    • (2006) J Biol Chem , vol.281 , pp. 30551-30560
    • Kaneko, R.1    Kato, H.2    Kawamura, Y.3    Esumi, S.4    Hirayama, T.5    Hirabayashi, T.6    Yagi, T.7
  • 25
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: automating chromatin-state discovery and characterization
    • Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9:215-6.
    • (2012) Nat Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 26
    • 84857331867 scopus 로고    scopus 로고
    • Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome
    • 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;148:816-31.
    • (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
    • 84940771118 scopus 로고    scopus 로고
    • Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations
    • Liu JZ, van Sommeren S, Huang H, Ng SC, Alberts R, Takahashi A, Ripke S, Lee JC, Jostins L, Shah T, et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet. 2015;47:979-86.
    • (2015) Nat Genet , vol.47 , pp. 979-986
    • Liu, J.Z.1    Sommeren, S.2    Huang, H.3    Ng, S.C.4    Alberts, R.5    Takahashi, A.6    Ripke, S.7    Lee, J.C.8    Jostins, L.9    Shah, T.10
  • 33
    • 84952975366 scopus 로고    scopus 로고
    • Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation
    • Busche S, Shao X, Caron M, Kwan T, Allum F, Cheung WA, Ge B, Westfall S, Simon MM, Multiple Tissue Human Expression Resource, et al. Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biol. 2015;16:290.
    • (2015) Genome Biol , vol.16 , pp. 290
    • Busche, S.1    Shao, X.2    Caron, M.3    Kwan, T.4    Allum, F.5    Cheung, W.A.6    Ge, B.7    Westfall, S.8    Simon, M.M.9
  • 35
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Consortium, E.P.1
  • 38
    • 0028807772 scopus 로고
    • EGEA (Epidemiological study on the Genetics and Environment of Asthma, bronchial hyperresponsiveness and atopy)--design issues. EGEA Co-operative Group
    • Kauffmann F, Dizier MH. EGEA (Epidemiological study on the Genetics and Environment of Asthma, bronchial hyperresponsiveness and atopy)--design issues. EGEA Co-operative Group. Clin Exp Allergy. 1995;25 Suppl 2:19-22.
    • (1995) Clin Exp Allergy , vol.25 , pp. 19-22
    • Kauffmann, F.1    Dizier, M.H.2
  • 43
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 44
    • 84868134071 scopus 로고    scopus 로고
    • Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing
    • Chapter 21, Unit21-23
    • Johnson MD, Mueller M, Game L, Aitman TJ. Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing. Curr Protoc Mol Biol. 2012;Chapter 21:Unit21-23.
    • (2012) Curr Protoc Mol Biol
    • Johnson, M.D.1    Mueller, M.2    Game, L.3    Aitman, T.J.4
  • 45
    • 84863565553 scopus 로고    scopus 로고
    • Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data
    • Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012;13:R61.
    • (2012) Genome Biol , vol.13 , pp. R61
    • Liu, Y.1    Siegmund, K.D.2    Laird, P.W.3    Berman, B.P.4
  • 46
    • 67651222400 scopus 로고    scopus 로고
    • A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    • Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009;5:e1000529.
    • (2009) PLoS Genet , vol.5
    • Howie, B.N.1    Donnelly, P.2    Marchini, J.3
  • 47
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003;100:9440-5.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 49
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-11.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 50
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 51
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq--a Python framework to work with high-throughput sequencing data
    • Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166-9.
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 52
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: a flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114-20.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 54
    • 0025066941 scopus 로고
    • More powerful procedures for multiple significance testing
    • Hochberg Y, Benjamini Y. More powerful procedures for multiple significance testing. Stat Med. 1990;9:811-8.
    • (1990) Stat Med , vol.9 , pp. 811-818
    • Hochberg, Y.1    Benjamini, Y.2
  • 56
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841-2.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.