EFORGE v2.0: Updated analysis of cell type-specific signal in epigenomic data

Charles E. Breeze; Alex P. Reynolds; Jenny Van Dongen; Ian Dunham; John Lazar; Shane Neph; Jeff Vierstra; Guillaume Bourque; Andrew E. Teschendorff; John A. Stamatoyannopoulos; Stephan Beck

doi:10.1093/bioinformatics/btz456

EFORGE v2.0: Updated analysis of cell type-specific signal in epigenomic data

Charles E. Breeze^*, Alex P. Reynolds, Jenny Van Dongen, Ian Dunham, John Lazar, Shane Neph, Jeff Vierstra, Guillaume Bourque, Andrew E. Teschendorff, John A. Stamatoyannopoulos, Stephan Beck

^*Corresponding author for this work

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

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.

Original language	English
Pages (from-to)	4767-4769
Number of pages	3
Journal	Bioinformatics
Volume	35
Issue number	22
DOIs	https://doi.org/10.1093/bioinformatics/btz456
Publication status	Published - 1 Nov 2019

Funding

C.E.B. was supported by a fellowship from the EU-FP7 project EpiTrain [316758]. Research in S.B.’s group was supported by the Wellcome Trust [99148]; Royal Society Wolfson Research Merit Award [WM100023] and EU-FP7 projects EpiTrain [316758]; EPIGENESYS [257082]; and BLUEPRINT [282510].

Funders	Funder number
EU-FP7
Wellcome Trust	99148
Seventh Framework Programme	257082, 316758, 282510

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/bioinformatics/btz456

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title = "EFORGE v2.0: Updated analysis of cell type-specific signal in epigenomic data",

abstract = "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.",

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doi = "10.1093/bioinformatics/btz456",

language = "English",

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T2 - Updated analysis of cell type-specific signal in epigenomic data

AU - Breeze, Charles E.

AU - Reynolds, Alex P.

AU - Van Dongen, Jenny

AU - Dunham, Ian

AU - Lazar, John

AU - Neph, Shane

AU - Vierstra, Jeff

AU - Bourque, Guillaume

AU - Teschendorff, Andrew E.

AU - Stamatoyannopoulos, John A.

AU - Beck, Stephan

PY - 2019/11/1

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EFORGE v2.0: Updated analysis of cell type-specific signal in epigenomic data

Abstract

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UN SDGs

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