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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/60202
Ver los metadatos del registro completo
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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 Técnicas2025-09-29T10:16:13Zoai: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:34982025-09-29 10:16:13.803CONICET 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/ |
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openAccess |
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application/pdf application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Nature Publishing Group |
publisher.none.fl_str_mv |
Nature Publishing Group |
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reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) |
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CONICET Digital (CONICET) |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
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dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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