Cis-regulatory elements are non-coding DNA sequences that control when, where, and how strongly nearby genes are expressed. They include enhancers, which boost transcription, and silencers, which suppress it. Identifying these elements across the genome is essential for understanding how cell-type-specific gene programs are established and how disease-associated genetic variants can disrupt gene regulation.
This track collection contains genome-wide computational predictions of cis-regulatory elements, including both enhancers and silencers, derived from deep learning models trained on chromatin accessibility and histone modification data. Each subtrack group covers a specific prediction method or publication. See the individual subtrack pages for details on methods, sample coverage, and data access.
TREDNet Candidate Enhancers and Silencers – Enhancers and silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples spanning primary cell types, cell lines, and tissues. Items are colored by the type of sample where the element is predominantly active. See the enhancer and silencer subtrack pages for full details.