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Updated: Jan 23, 2026

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TChIP-Seq: Cell-Type-Specific Epigenome Profiling
Published on: January 23, 2019
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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.
Bioinformatics (Oxford, England)
|June 5, 2019
Summary
The enhanced eFORGE v2.0 tool now analyzes DNA methylation data from both Illumina EPIC and 450k arrays. This updated method offers new insights into epigenome-wide association studies and epigenome editing.
Area of Science:
- Genomics
- Epigenetics
- Bioinformatics
Background:
- The Illumina Infinium EPIC BeadChip expands DNA methylation analysis with over 400,000 new sites compared to the 450k array.
- The eFORGE method previously provided cell type-specific insights for 450k array data.
Purpose of the Study:
- To present an updated and improved version of the eFORGE method.
- To enable analysis of both EPIC and 450k array DNA methylation data.
- To incorporate new features for enhanced epigenome-wide association study interpretation.
Main Methods:
- Development of eFORGE v2.0, a web-based tool.
- Integration of analysis for Illumina Infinium EPIC BeadChip and 450k array data.
- Inclusion of chromatin states, transcription factor motifs, and DNase I footprints analysis.
Main Results:
- eFORGE v2.0 supports analysis of both EPIC and 450k array data.
- New analytical features provide deeper insights into epigenomic data.
- The tool facilitates interpretation of epigenome-wide association studies.
Conclusions:
- eFORGE v2.0 is a powerful, updated tool for DNA methylation analysis.
- The enhanced features support advanced epigenome research and interpretation.
- The web tool is readily accessible for the scientific community.
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