ENCODEannotated

ENCODEannotated is a community-driven, integrated collection of annotations derived from ENCODE project data, intended to enable standardized interpretation of regulatory elements across experiments and cell types. The resource curates and harmonizes ENCODE outputs such as DNase I hypersensitivity sites, histone modification maps, transcription factor binding profiles, and RNA expression data into unified annotation sets. It additionally incorporates chromatin state segmentations—for example promoter and enhancer maps—from methods like ChromHMM or Segway, mapped to common genome builds to support cross-study comparisons.

Data are annotated with rich metadata, including cell type, tissue context, assay type, experimental conditions, and versioning information. ENCODEannotated provides multiple access patterns: a centralized web portal, programmatic REST API, downloadable formats (BED, GFF3, bigWig/bigBed), and genome-browser track hubs.

Common use cases include annotating genetic variants to predict regulatory impact, inferring gene regulation networks, and enabling meta-analyses across ENCODE experiments. The resource also supports reproducibility through provenance records and versioned releases.

Limitations include incomplete coverage across the full ENCODE catalog, variability in assay depth and quality, and reliance on existing ENCODE pipelines and genome coordinates. Users should interpret annotations in the context of cell type and experimental conditions.

ENCODEannotated is not an official ENCODE product, but a community resource that builds on ENCODE data with standardized annotations and documentation. It aims to complement ENCODE by lowering barriers to integration and comparative analyses, while encouraging citation of original datasets.