MethylMix 2.0: An R package for identifying DNA methylation genes

Autores
Cedoz, Pierre Louis; Prunello, Marcos Miguel; Brennan, Kevin; Gevaert, Olivier
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, highthroughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. Here we present a new version of MethylMix that automates the construction of DNA-methylation and gene expression datasets from The Cancer Genome Atlas (TCGA). More precisely, MethylMix 2.0 incorporates two major updates: The automated downloading of DNA methylation and gene expression datasets from TCGA and the automated preprocessing of such datasets: Value imputation, batch correction and CpG sites clustering within each gene. The resulting datasets can subsequently be analyzed with MethylMix to identify transcriptionally predictive methylation states.
Fil: Cedoz, Pierre Louis. University of Stanford; Estados Unidos
Fil: Prunello, Marcos Miguel. Universidad Nacional de Rosario; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina
Fil: Brennan, Kevin. University of Stanford; Estados Unidos
Fil: Gevaert, Olivier. University of Stanford; Estados Unidos
Materia
R PACKAGE
BIOCONDUCTOR
DNA METHYLATION
CANCER SUBTYPING
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:11336/95135
Acceder
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network_name_str CONICET Digital (CONICET)
spelling MethylMix 2.0: An R package for identifying DNA methylation genesCedoz, Pierre LouisPrunello, Marcos MiguelBrennan, KevinGevaert, OlivierR PACKAGEBIOCONDUCTORDNA METHYLATIONCANCER SUBTYPINGhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, highthroughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. Here we present a new version of MethylMix that automates the construction of DNA-methylation and gene expression datasets from The Cancer Genome Atlas (TCGA). More precisely, MethylMix 2.0 incorporates two major updates: The automated downloading of DNA methylation and gene expression datasets from TCGA and the automated preprocessing of such datasets: Value imputation, batch correction and CpG sites clustering within each gene. The resulting datasets can subsequently be analyzed with MethylMix to identify transcriptionally predictive methylation states.Fil: Cedoz, Pierre Louis. University of Stanford; Estados UnidosFil: Prunello, Marcos Miguel. Universidad Nacional de Rosario; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; ArgentinaFil: Brennan, Kevin. University of Stanford; Estados UnidosFil: Gevaert, Olivier. University of Stanford; Estados UnidosOxford University Press2018-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/95135Cedoz, Pierre Louis; Prunello, Marcos Miguel; Brennan, Kevin; Gevaert, Olivier; MethylMix 2.0: An R package for identifying DNA methylation genes; Oxford University Press; Bioinformatics (Oxford, England); 34; 17; 9-2018; 3044-30461367-4803CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/bioinformatics/article/34/17/3044/4970512info:eu-repo/semantics/altIdentifier/doi/10.1093/bioinformatics/bty156info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:27:50Zoai:ri.conicet.gov.ar:11336/95135instacron: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 14:27:50.483CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv MethylMix 2.0: An R package for identifying DNA methylation genes
title MethylMix 2.0: An R package for identifying DNA methylation genes
spellingShingle MethylMix 2.0: An R package for identifying DNA methylation genes
Cedoz, Pierre Louis
R PACKAGE
BIOCONDUCTOR
DNA METHYLATION
CANCER SUBTYPING
title_short MethylMix 2.0: An R package for identifying DNA methylation genes
title_full MethylMix 2.0: An R package for identifying DNA methylation genes
title_fullStr MethylMix 2.0: An R package for identifying DNA methylation genes
title_full_unstemmed MethylMix 2.0: An R package for identifying DNA methylation genes
title_sort MethylMix 2.0: An R package for identifying DNA methylation genes
dc.creator.none.fl_str_mv Cedoz, Pierre Louis
Prunello, Marcos Miguel
Brennan, Kevin
Gevaert, Olivier
author Cedoz, Pierre Louis
author_facet Cedoz, Pierre Louis
Prunello, Marcos Miguel
Brennan, Kevin
Gevaert, Olivier
author_role author
author2 Prunello, Marcos Miguel
Brennan, Kevin
Gevaert, Olivier
author2_role author
author
author
dc.subject.none.fl_str_mv R PACKAGE
BIOCONDUCTOR
DNA METHYLATION
CANCER SUBTYPING
topic R PACKAGE
BIOCONDUCTOR
DNA METHYLATION
CANCER SUBTYPING
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, highthroughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. Here we present a new version of MethylMix that automates the construction of DNA-methylation and gene expression datasets from The Cancer Genome Atlas (TCGA). More precisely, MethylMix 2.0 incorporates two major updates: The automated downloading of DNA methylation and gene expression datasets from TCGA and the automated preprocessing of such datasets: Value imputation, batch correction and CpG sites clustering within each gene. The resulting datasets can subsequently be analyzed with MethylMix to identify transcriptionally predictive methylation states.
Fil: Cedoz, Pierre Louis. University of Stanford; Estados Unidos
Fil: Prunello, Marcos Miguel. Universidad Nacional de Rosario; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina
Fil: Brennan, Kevin. University of Stanford; Estados Unidos
Fil: Gevaert, Olivier. University of Stanford; Estados Unidos
description Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, highthroughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. Here we present a new version of MethylMix that automates the construction of DNA-methylation and gene expression datasets from The Cancer Genome Atlas (TCGA). More precisely, MethylMix 2.0 incorporates two major updates: The automated downloading of DNA methylation and gene expression datasets from TCGA and the automated preprocessing of such datasets: Value imputation, batch correction and CpG sites clustering within each gene. The resulting datasets can subsequently be analyzed with MethylMix to identify transcriptionally predictive methylation states.
publishDate 2018
dc.date.none.fl_str_mv 2018-09
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/11336/95135
Cedoz, Pierre Louis; Prunello, Marcos Miguel; Brennan, Kevin; Gevaert, Olivier; MethylMix 2.0: An R package for identifying DNA methylation genes; Oxford University Press; Bioinformatics (Oxford, England); 34; 17; 9-2018; 3044-3046
1367-4803
CONICET Digital
CONICET
url http://hdl.handle.net/11336/95135
identifier_str_mv Cedoz, Pierre Louis; Prunello, Marcos Miguel; Brennan, Kevin; Gevaert, Olivier; MethylMix 2.0: An R package for identifying DNA methylation genes; Oxford University Press; Bioinformatics (Oxford, England); 34; 17; 9-2018; 3044-3046
1367-4803
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/bioinformatics/article/34/17/3044/4970512
info:eu-repo/semantics/altIdentifier/doi/10.1093/bioinformatics/bty156
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 Oxford University Press
publisher.none.fl_str_mv Oxford University 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 13.22299

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