nonENCODE

nonENCODE is a descriptor used in genomics to denote data, analyses, or resources that are not produced or included within the ENCODE project. It is not a formal project or organization, but rather a label used in discussions and studies that contrast ENCODE-derived annotations with alternative sources.

In practice, nonENCODE can refer to datasets from other consortia, individual laboratories, or computational predictions that address gene regulation, chromatin state, or transcriptional activity but do not follow ENCODE’s specific experimental assays or processing pipelines. It is often used when evaluating how well ENCODE annotations cover regulatory elements compared to other data.

Because ENCODE has established particular experimental approaches and metadata standards, nonENCODE data may vary in assay type, depth, processing, and annotation. Integrative analyses that combine ENCODE and nonENCODE sources may require harmonization and careful quality control to avoid biases and ensure comparability.

The term is informal and can be ambiguous; its precise meaning depends on the study context. Researchers should define what qualifies as nonENCODE in a given analysis and consider reproducibility when comparing to ENCODE data.

See also ENCODE Project, modENCODE, Roadmap Epigenomics, functional genomics.