eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data-Reference-Cited by-同舟云学术

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

Published:2019-06-04 Issue:22 Volume:35 Page:4767-4769
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Breeze Charles E¹²^ORCID,Reynolds Alex P²,van Dongen Jenny³,Dunham Ian⁴,Lazar John²,Neph Shane²,Vierstra Jeff²,Bourque Guillaume⁵^ORCID,Teschendorff Andrew E⁶⁷,Stamatoyannopoulos John A²,Beck Stephan¹

Affiliation:

1. Medical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK

2. Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA

3. Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam 1081BT, The Netherlands

4. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK

5. Department of Human Genetics, McGill University and Génome Québec Innovation Center, Montréal H3A 0G1, Canada

6. CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China

7. Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK

Abstract

Abstract 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.

Funder

EpiTrain

Wellcome Trust

Royal Society Wolfson Research Merit Award

EPIGENESYS

BLUEPRINT

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz456/28837676/btz456.pdf

Reference6 articles.

1. An atlas of active enhancers across human cell types and tissues;Andersson;Nature,2014

2. eFORGE: a tool for identifying cell type-specific signal in epigenomic data;Breeze;Cell Rep,2016

3. An integrated encyclopedia of DNA elements in the human genome;Nature,2012

4. Validation of a DNA methylation microarray for 850, 000 CpG sites of the human genome enriched in enhancer sequences;Moran;Epigenomics,2016

5. DNA methylation: roles in mammalian development;Smith;Nat. Rev. Genet,2013

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