eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.
basic_science · Level V
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- Record sourced from PubMed, PMID 31161210.
- Also identified by DOI 10.1093/bioinformatics/btz456 and PMC identifier 6853678.
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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. eFORGE v2.0 is implemented as a web tool available from https://eforge.altiusinstitute.org and https://eforge-tf.altiusinstitute.org/. Supplementary data are available at Bioinformatics online.
Medical subject headings
- DNA Methylation
- Epigenomics