eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data

SUMMARY: The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over 400 000 new sites. Previously, a method named eFORGE was developed to provide insights into cell type-specific and cell-composition effects for 450k data...

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Autores principales: Breeze, Charles E, Reynolds, Alex P, van Dongen, Jenny, Dunham, Ian, Lazar, John, Neph, Shane, Vierstra, Jeff, Bourque, Guillaume, Teschendorff, Andrew E, Stamatoyannopoulos, John A, Beck, Stephan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853678/
https://www.ncbi.nlm.nih.gov/pubmed/31161210
http://dx.doi.org/10.1093/bioinformatics/btz456
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author Breeze, Charles E
Reynolds, Alex P
van Dongen, Jenny
Dunham, Ian
Lazar, John
Neph, Shane
Vierstra, Jeff
Bourque, Guillaume
Teschendorff, Andrew E
Stamatoyannopoulos, John A
Beck, Stephan
author_facet Breeze, Charles E
Reynolds, Alex P
van Dongen, Jenny
Dunham, Ian
Lazar, John
Neph, Shane
Vierstra, Jeff
Bourque, Guillaume
Teschendorff, Andrew E
Stamatoyannopoulos, John A
Beck, Stephan
author_sort Breeze, Charles E
collection PubMed
description SUMMARY: The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over 400 000 new sites. Previously, a method named eFORGE was developed to provide insights into cell type-specific and cell-composition effects for 450k data. Here, we present a significantly updated and improved version of eFORGE that can analyze both EPIC and 450k array data. New features include analysis of chromatin states, transcription factor motifs and DNase I footprints, providing tools for epigenome-wide association study interpretation and epigenome editing. AVAILABILITY AND IMPLEMENTATION: eFORGE v2.0 is implemented as a web tool available from https://eforge.altiusinstitute.org and https://eforge-tf.altiusinstitute.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-68536782019-11-19 eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data Breeze, Charles E Reynolds, Alex P van Dongen, Jenny Dunham, Ian Lazar, John Neph, Shane Vierstra, Jeff Bourque, Guillaume Teschendorff, Andrew E Stamatoyannopoulos, John A Beck, Stephan Bioinformatics Applications Notes SUMMARY: The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over 400 000 new sites. Previously, a method named eFORGE was developed to provide insights into cell type-specific and cell-composition effects for 450k data. Here, we present a significantly updated and improved version of eFORGE that can analyze both EPIC and 450k array data. New features include analysis of chromatin states, transcription factor motifs and DNase I footprints, providing tools for epigenome-wide association study interpretation and epigenome editing. AVAILABILITY AND IMPLEMENTATION: eFORGE v2.0 is implemented as a web tool available from https://eforge.altiusinstitute.org and https://eforge-tf.altiusinstitute.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2019-11-15 2019-06-04 /pmc/articles/PMC6853678/ /pubmed/31161210 http://dx.doi.org/10.1093/bioinformatics/btz456 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Breeze, Charles E
Reynolds, Alex P
van Dongen, Jenny
Dunham, Ian
Lazar, John
Neph, Shane
Vierstra, Jeff
Bourque, Guillaume
Teschendorff, Andrew E
Stamatoyannopoulos, John A
Beck, Stephan
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
title eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
title_full eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
title_fullStr eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
title_full_unstemmed eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
title_short eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
title_sort eforge v2.0: updated analysis of cell type-specific signal in epigenomic data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853678/
https://www.ncbi.nlm.nih.gov/pubmed/31161210
http://dx.doi.org/10.1093/bioinformatics/btz456
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