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Updated: Jan 23, 2026

TChIP-Seq: Cell-Type-Specific Epigenome Profiling
Published on: January 23, 2019
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
Charles E Breeze1,2, Alex P Reynolds2, Jenny van Dongen3
1Medical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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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