An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

Autores
Rakyan, Vardhman K.; Down, Thomas A.; Thorne, Natalie P.; Flicek, Paul; Kulesha, Eugene; Gräf, Stefan; Tomazou, Eleni M.; Bäckdahl, Liselotte; Johnson, Nathan; Herberth, Marlis; Howe, Kevin L.; Jackson, David K.; Miretti, Marcos Mateo; Fiegler, Heike; Marioni, John C.; Birney, Ewan; Hubbard, Tim J. P.; Carter, Nigel P.; Tavaré, Simon; Beck, Stephan G.
Año de publicación
2008
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications. ©2008 by Cold Spring Harbor Laboratory Press.
Fil: Rakyan, Vardhman K.. Barts And The London School Of Medicine And Dentistry;
Fil: Down, Thomas A.. University of Cambridge; Estados Unidos
Fil: Thorne, Natalie P.. University of Cambridge; Estados Unidos
Fil: Flicek, Paul. European Bioinformatics Institute;
Fil: Kulesha, Eugene. European Bioinformatics Institute;
Fil: Gräf, Stefan. European Bioinformatics Institute;
Fil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute;
Fil: Bäckdahl, Liselotte. Ucl Cancer Institute;
Fil: Johnson, Nathan. European Bioinformatics Institute;
Fil: Herberth, Marlis. University of Cambridge; Estados Unidos
Fil: Howe, Kevin L.. University of Cambridge; Estados Unidos
Fil: Jackson, David K.. Wellcome Trust Sanger Institute;
Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina
Fil: Fiegler, Heike. Roche Diagnostics Ltd.; . Wellcome Trust Sanger Institute;
Fil: Marioni, John C.. University of Cambridge; Estados Unidos
Fil: Birney, Ewan. European Bioinformatics Institute;
Fil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute;
Fil: Carter, Nigel P.. Wellcome Trust Sanger Institute;
Fil: Tavaré, Simon. University of Cambridge; Estados Unidos
Fil: Beck, Stephan G.. Ucl Cancer Institute;
Materia
tissue specific methylation
tDMRs
methylome
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:11336/60916
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/60916
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)Rakyan, Vardhman K.Down, Thomas A.Thorne, Natalie P.Flicek, PaulKulesha, EugeneGräf, StefanTomazou, Eleni M.Bäckdahl, LiselotteJohnson, NathanHerberth, MarlisHowe, Kevin L.Jackson, David K.Miretti, Marcos MateoFiegler, HeikeMarioni, John C.Birney, EwanHubbard, Tim J. P.Carter, Nigel P.Tavaré, SimonBeck, Stephan G.tissue specific methylationtDMRsmethylomehttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications. ©2008 by Cold Spring Harbor Laboratory Press.Fil: Rakyan, Vardhman K.. Barts And The London School Of Medicine And Dentistry;Fil: Down, Thomas A.. University of Cambridge; Estados UnidosFil: Thorne, Natalie P.. University of Cambridge; Estados UnidosFil: Flicek, Paul. European Bioinformatics Institute;Fil: Kulesha, Eugene. European Bioinformatics Institute;Fil: Gräf, Stefan. European Bioinformatics Institute;Fil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute;Fil: Bäckdahl, Liselotte. Ucl Cancer Institute;Fil: Johnson, Nathan. European Bioinformatics Institute;Fil: Herberth, Marlis. University of Cambridge; Estados UnidosFil: Howe, Kevin L.. University of Cambridge; Estados UnidosFil: Jackson, David K.. Wellcome Trust Sanger Institute;Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Fiegler, Heike. Roche Diagnostics Ltd.; . Wellcome Trust Sanger Institute;Fil: Marioni, John C.. University of Cambridge; Estados UnidosFil: Birney, Ewan. European Bioinformatics Institute;Fil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute;Fil: Carter, Nigel P.. Wellcome Trust Sanger Institute;Fil: Tavaré, Simon. University of Cambridge; Estados UnidosFil: Beck, Stephan G.. Ucl Cancer Institute;Cold Spring Harbor Laboratory Press2008-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/60916Rakyan, Vardhman K.; Down, Thomas A.; Thorne, Natalie P.; Flicek, Paul; Kulesha, Eugene; et al.; An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs); Cold Spring Harbor Laboratory Press; Genome Research; 18; 9; 9-2008; 1518-15291088-9051CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1101/gr.077479.108info:eu-repo/semantics/altIdentifier/url/https://genome.cshlp.org/content/18/9/1518info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:47:45Zoai:ri.conicet.gov.ar:11336/60916instacron: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 10:47:45.34CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
title An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
spellingShingle An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
Rakyan, Vardhman K.
tissue specific methylation
tDMRs
methylome
title_short An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
title_full An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
title_fullStr An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
title_full_unstemmed An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
title_sort An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
dc.creator.none.fl_str_mv Rakyan, Vardhman K.
Down, Thomas A.
Thorne, Natalie P.
Flicek, Paul
Kulesha, Eugene
Gräf, Stefan
Tomazou, Eleni M.
Bäckdahl, Liselotte
Johnson, Nathan
Herberth, Marlis
Howe, Kevin L.
Jackson, David K.
Miretti, Marcos Mateo
Fiegler, Heike
Marioni, John C.
Birney, Ewan
Hubbard, Tim J. P.
Carter, Nigel P.
Tavaré, Simon
Beck, Stephan G.
author Rakyan, Vardhman K.
author_facet Rakyan, Vardhman K.
Down, Thomas A.
Thorne, Natalie P.
Flicek, Paul
Kulesha, Eugene
Gräf, Stefan
Tomazou, Eleni M.
Bäckdahl, Liselotte
Johnson, Nathan
Herberth, Marlis
Howe, Kevin L.
Jackson, David K.
Miretti, Marcos Mateo
Fiegler, Heike
Marioni, John C.
Birney, Ewan
Hubbard, Tim J. P.
Carter, Nigel P.
Tavaré, Simon
Beck, Stephan G.
author_role author
author2 Down, Thomas A.
Thorne, Natalie P.
Flicek, Paul
Kulesha, Eugene
Gräf, Stefan
Tomazou, Eleni M.
Bäckdahl, Liselotte
Johnson, Nathan
Herberth, Marlis
Howe, Kevin L.
Jackson, David K.
Miretti, Marcos Mateo
Fiegler, Heike
Marioni, John C.
Birney, Ewan
Hubbard, Tim J. P.
Carter, Nigel P.
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
dc.subject.none.fl_str_mv tissue specific methylation
tDMRs
methylome
topic tissue specific methylation
tDMRs
methylome
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications. ©2008 by Cold Spring Harbor Laboratory Press.
Fil: Rakyan, Vardhman K.. Barts And The London School Of Medicine And Dentistry;
Fil: Down, Thomas A.. University of Cambridge; Estados Unidos
Fil: Thorne, Natalie P.. University of Cambridge; Estados Unidos
Fil: Flicek, Paul. European Bioinformatics Institute;
Fil: Kulesha, Eugene. European Bioinformatics Institute;
Fil: Gräf, Stefan. European Bioinformatics Institute;
Fil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute;
Fil: Bäckdahl, Liselotte. Ucl Cancer Institute;
Fil: Johnson, Nathan. European Bioinformatics Institute;
Fil: Herberth, Marlis. University of Cambridge; Estados Unidos
Fil: Howe, Kevin L.. University of Cambridge; Estados Unidos
Fil: Jackson, David K.. Wellcome Trust Sanger Institute;
Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina
Fil: Fiegler, Heike. Roche Diagnostics Ltd.; . Wellcome Trust Sanger Institute;
Fil: Marioni, John C.. University of Cambridge; Estados Unidos
Fil: Birney, Ewan. European Bioinformatics Institute;
Fil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute;
Fil: Carter, Nigel P.. Wellcome Trust Sanger Institute;
Fil: Tavaré, Simon. University of Cambridge; Estados Unidos
Fil: Beck, Stephan G.. Ucl Cancer Institute;
description We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications. ©2008 by Cold Spring Harbor Laboratory Press.
publishDate 2008
dc.date.none.fl_str_mv 2008-09
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/11336/60916
Rakyan, Vardhman K.; Down, Thomas A.; Thorne, Natalie P.; Flicek, Paul; Kulesha, Eugene; et al.; An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs); Cold Spring Harbor Laboratory Press; Genome Research; 18; 9; 9-2008; 1518-1529
1088-9051
CONICET Digital
CONICET
url http://hdl.handle.net/11336/60916
identifier_str_mv Rakyan, Vardhman K.; Down, Thomas A.; Thorne, Natalie P.; Flicek, Paul; Kulesha, Eugene; et al.; An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs); Cold Spring Harbor Laboratory Press; Genome Research; 18; 9; 9-2008; 1518-1529
1088-9051
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1101/gr.077479.108
info:eu-repo/semantics/altIdentifier/url/https://genome.cshlp.org/content/18/9/1518
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
dc.publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
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 13.070432

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