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

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.

SUBMITTER: Breeze CE

PROVIDER: S-EPMC6853678 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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

Breeze Charles E CE Reynolds Alex P AP van Dongen Jenny J Dunham Ian I Lazar John J Neph Shane S Vierstra Jeff J Bourque Guillaume G Teschendorff Andrew E AE Stamatoyannopoulos John A JA Beck Stephan S

Bioinformatics (Oxford, England) 20191101 22

<h4>Summary</h4>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 ...[more]

PMID: 31161210

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