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]

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)

SDG 12 Responsible Consumption and Production

Access to Document

10.1093/bioinformatics/btz456

Persistent URL (handle)

Persistent link

Cite this

@article{7f2f32a3e1a044b2a43a5a3c47351c64,

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.",

author = "Breeze, \{Charles E.\} and Reynolds, \{Alex P.\} and \{Van Dongen\}, Jenny and Ian Dunham and John Lazar and Shane Neph and Jeff Vierstra and Guillaume Bourque and Teschendorff, \{Andrew E.\} and Stamatoyannopoulos, \{John A.\} and Stephan Beck",

year = "2019",

month = nov,

day = "1",

doi = "10.1093/bioinformatics/btz456",

language = "English",

volume = "35",

pages = "4767--4769",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "22",

}

TY - JOUR

T1 - EFORGE v2.0

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

Y1 - 2019/11/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85074964176

UR - https://www.scopus.com/pages/publications/85074964176#tab=citedBy

U2 - 10.1093/bioinformatics/btz456

DO - 10.1093/bioinformatics/btz456

M3 - Article

C2 - 31161210

AN - SCOPUS:85074964176

SN - 1367-4803

VL - 35

SP - 4767

EP - 4769

JO - Bioinformatics

JF - Bioinformatics

IS - 22

ER -

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

Abstract

Funding

UN SDGs

Access to Document

Persistent URL (handle)

Other files and links

Fingerprint

Cite this