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

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...

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Detalles Bibliográficos
Autores principales: Breeze, Charles E, Reynolds, Alex P, van Dongen, Jenny, Dunham, Ian, Lazar, John, Neph, Shane, Vierstra, Jeff, Bourque, Guillaume, Teschendorff, Andrew E, Stamatoyannopoulos, John A, Beck, Stephan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853678/
https://www.ncbi.nlm.nih.gov/pubmed/31161210
http://dx.doi.org/10.1093/bioinformatics/btz456
Descripción
Sumario: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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