An integrated encyclopedia of DNA elements in the human genome.
Nature. 2012 Sep 6;489(7414):57-74.
- Abstract
- The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
- References
Related data
- Available data
- peak calls
- File format
- BED
- Data summary
- Functional genomics experiments based on next-gen sequencing (e.g. ChIP-seq, MNase-seq, DNase-seq, FAIRE-seq) that measure biochemical activity of various elements in the genome often produce artifact signal in certain regions of the genome. The authors identify a comprehensive set of regions in the human genome that have anomalous, unstructured, high signal/read counts in next generation sequencing experiments independent of cell line and type of experiment. These blacklists are applicable to functional genomic data based on short-read sequencing (20-100bp reads). These are not directly applicable to RNA-seq or any other transcriptome data types.