A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

Autores
Down, Thomas A.; Rakyan, Vardhman K.; Turner, Daniel J.; Flicek, Paul; Li, Heng; Kulesha, Eugene; Gräf, Stefan; Johnson, Nathan; Herrero, Javier; Tomazou, Eleni M.; Thorne, Natalie P.; Bäckdahl, Liselotte; Herberth, Marlis; Howe, Kevin L.; Jackson, David K.; Miretti, Marcos Mateo; Marioni, John C.; Birney, Ewan; Hubbard, Tim J. P.; Durbin, Richard; Tavaré, Simon; Beck, Stephan G.
Año de publicación
2008
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm - Bayesian tool for methylation analysis (Batman) - for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation. © 2008 Nature Publishing Group.
Fil: Down, Thomas A.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Rakyan, Vardhman K.. Institute of Cell and Molecular Science; Reino Unido
Fil: Turner, Daniel J.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Flicek, Paul. European Bioinformatics Institute; Reino Unido
Fil: Li, Heng. Wellcome Trust Sanger Institute; Reino Unido
Fil: Kulesha, Eugene. European Bioinformatics Institute; Reino Unido
Fil: Gräf, Stefan. European Bioinformatics Institute; Reino Unido
Fil: Johnson, Nathan. European Bioinformatics Institute; Reino Unido
Fil: Herrero, Javier. European Bioinformatics Institute; Reino Unido
Fil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Thorne, Natalie P.. University of Cambridge; Reino Unido
Fil: Bäckdahl, Liselotte. University College London; Reino Unido
Fil: Herberth, Marlis. University of Cambridge; Reino Unido
Fil: Howe, Kevin L.. University of Cambridge; Reino Unido
Fil: Jackson, David K.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Wellcome Trust Sanger Institute; Reino Unido
Fil: Marioni, John C.. University of Cambridge; Reino Unido
Fil: Birney, Ewan. European Bioinformatics Institute; Reino Unido
Fil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Durbin, Richard. Wellcome Trust Sanger Institute; Reino Unido
Fil: Tavaré, Simon. University of Cambridge; Reino Unido
Fil: Beck, Stephan G.. University College London; Reino Unido
Materia
Tissue-Specific Methylation
Tdmrs
Bayesian Deconvolution
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/60202
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/60202
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysisDown, Thomas A.Rakyan, Vardhman K.Turner, Daniel J.Flicek, PaulLi, HengKulesha, EugeneGräf, StefanJohnson, NathanHerrero, JavierTomazou, Eleni M.Thorne, Natalie P.Bäckdahl, LiselotteHerberth, MarlisHowe, Kevin L.Jackson, David K.Miretti, Marcos MateoMarioni, John C.Birney, EwanHubbard, Tim J. P.Durbin, RichardTavaré, SimonBeck, Stephan G.Tissue-Specific MethylationTdmrsBayesian Deconvolutionhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm - Bayesian tool for methylation analysis (Batman) - for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation. © 2008 Nature Publishing Group.Fil: Down, Thomas A.. Wellcome Trust Sanger Institute; Reino UnidoFil: Rakyan, Vardhman K.. Institute of Cell and Molecular Science; Reino UnidoFil: Turner, Daniel J.. Wellcome Trust Sanger Institute; Reino UnidoFil: Flicek, Paul. European Bioinformatics Institute; Reino UnidoFil: Li, Heng. Wellcome Trust Sanger Institute; Reino UnidoFil: Kulesha, Eugene. European Bioinformatics Institute; Reino UnidoFil: Gräf, Stefan. European Bioinformatics Institute; Reino UnidoFil: Johnson, Nathan. European Bioinformatics Institute; Reino UnidoFil: Herrero, Javier. European Bioinformatics Institute; Reino UnidoFil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute; Reino UnidoFil: Thorne, Natalie P.. University of Cambridge; Reino UnidoFil: Bäckdahl, Liselotte. University College London; Reino UnidoFil: Herberth, Marlis. University of Cambridge; Reino UnidoFil: Howe, Kevin L.. University of Cambridge; Reino UnidoFil: Jackson, David K.. Wellcome Trust Sanger Institute; Reino UnidoFil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Wellcome Trust Sanger Institute; Reino UnidoFil: Marioni, John C.. University of Cambridge; Reino UnidoFil: Birney, Ewan. European Bioinformatics Institute; Reino UnidoFil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute; Reino UnidoFil: Durbin, Richard. Wellcome Trust Sanger Institute; Reino UnidoFil: Tavaré, Simon. University of Cambridge; Reino UnidoFil: Beck, Stephan G.. University College London; Reino UnidoNature Publishing Group2008-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/60202Down, Thomas A.; Rakyan, Vardhman K.; Turner, Daniel J.; Flicek, Paul; Li, Heng; et al.; A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis; Nature Publishing Group; Nature Biotechnology; 26; 7; 7-2008; 779-7851087-0156CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1038/nbt1414info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/nbt1414info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:13:29Zoai:ri.conicet.gov.ar:11336/60202instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 15:13:29.504CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
title A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
spellingShingle A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Down, Thomas A.
Tissue-Specific Methylation
Tdmrs
Bayesian Deconvolution
title_short A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
title_full A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
title_fullStr A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
title_full_unstemmed A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
title_sort A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
dc.creator.none.fl_str_mv Down, Thomas A.
Rakyan, Vardhman K.
Turner, Daniel J.
Flicek, Paul
Li, Heng
Kulesha, Eugene
Gräf, Stefan
Johnson, Nathan
Herrero, Javier
Tomazou, Eleni M.
Thorne, Natalie P.
Bäckdahl, Liselotte
Herberth, Marlis
Howe, Kevin L.
Jackson, David K.
Miretti, Marcos Mateo
Marioni, John C.
Birney, Ewan
Hubbard, Tim J. P.
Durbin, Richard
Tavaré, Simon
Beck, Stephan G.
author Down, Thomas A.
author_facet Down, Thomas A.
Rakyan, Vardhman K.
Turner, Daniel J.
Flicek, Paul
Li, Heng
Kulesha, Eugene
Gräf, Stefan
Johnson, Nathan
Herrero, Javier
Tomazou, Eleni M.
Thorne, Natalie P.
Bäckdahl, Liselotte
Herberth, Marlis
Howe, Kevin L.
Jackson, David K.
Miretti, Marcos Mateo
Marioni, John C.
Birney, Ewan
Hubbard, Tim J. P.
Durbin, Richard
Tavaré, Simon
Beck, Stephan G.
author_role author
author2 Rakyan, Vardhman K.
Turner, Daniel J.
Flicek, Paul
Li, Heng
Kulesha, Eugene
Gräf, Stefan
Johnson, Nathan
Herrero, Javier
Tomazou, Eleni M.
Thorne, Natalie P.
Bäckdahl, Liselotte
Herberth, Marlis
Howe, Kevin L.
Jackson, David K.
Miretti, Marcos Mateo
Marioni, John C.
Birney, Ewan
Hubbard, Tim J. P.
Durbin, Richard
Tavaré, Simon
Beck, Stephan G.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Tissue-Specific Methylation
Tdmrs
Bayesian Deconvolution
topic Tissue-Specific Methylation
Tdmrs
Bayesian Deconvolution
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm - Bayesian tool for methylation analysis (Batman) - for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation. © 2008 Nature Publishing Group.
Fil: Down, Thomas A.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Rakyan, Vardhman K.. Institute of Cell and Molecular Science; Reino Unido
Fil: Turner, Daniel J.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Flicek, Paul. European Bioinformatics Institute; Reino Unido
Fil: Li, Heng. Wellcome Trust Sanger Institute; Reino Unido
Fil: Kulesha, Eugene. European Bioinformatics Institute; Reino Unido
Fil: Gräf, Stefan. European Bioinformatics Institute; Reino Unido
Fil: Johnson, Nathan. European Bioinformatics Institute; Reino Unido
Fil: Herrero, Javier. European Bioinformatics Institute; Reino Unido
Fil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Thorne, Natalie P.. University of Cambridge; Reino Unido
Fil: Bäckdahl, Liselotte. University College London; Reino Unido
Fil: Herberth, Marlis. University of Cambridge; Reino Unido
Fil: Howe, Kevin L.. University of Cambridge; Reino Unido
Fil: Jackson, David K.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Wellcome Trust Sanger Institute; Reino Unido
Fil: Marioni, John C.. University of Cambridge; Reino Unido
Fil: Birney, Ewan. European Bioinformatics Institute; Reino Unido
Fil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute; Reino Unido
Fil: Durbin, Richard. Wellcome Trust Sanger Institute; Reino Unido
Fil: Tavaré, Simon. University of Cambridge; Reino Unido
Fil: Beck, Stephan G.. University College London; Reino Unido
description DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm - Bayesian tool for methylation analysis (Batman) - for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation. © 2008 Nature Publishing Group.
publishDate 2008
dc.date.none.fl_str_mv 2008-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/60202
Down, Thomas A.; Rakyan, Vardhman K.; Turner, Daniel J.; Flicek, Paul; Li, Heng; et al.; A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis; Nature Publishing Group; Nature Biotechnology; 26; 7; 7-2008; 779-785
1087-0156
CONICET Digital
CONICET
url http://hdl.handle.net/11336/60202
identifier_str_mv Down, Thomas A.; Rakyan, Vardhman K.; Turner, Daniel J.; Flicek, Paul; Li, Heng; et al.; A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis; Nature Publishing Group; Nature Biotechnology; 26; 7; 7-2008; 779-785
1087-0156
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1038/nbt1414
info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/nbt1414
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.22299

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