Ensembl regulation resources
By Daniel R. Zerbino, Nathan Johnson, Thomas Juetteman, Daniel Sheppard, Steven P. Wilder, Ilias Lavidas, M. Nuhn, Emily Perry, Quentin Raffaillac-Desfosses, D. Sobral and 12 more. 2016
64 citations recorded by the source corpus.
New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study of their fluctuations should provide insights into gene expression regulation, cell differentiation and disease. The Ensembl project collects and maintains the Ensembl regulation data resources on epigenetic marks, transcription factor binding and DNA methylation for human and mouse, as well as microarray probe mappings and annotations for a variety of chordate genomes. From this data, we produce a functional annotation of the regulatory elements along the human and mouse genomes with plans to expand to other species as data becomes available. Starting from well-studied cell lines, we will progressively expand our library of measurements to a greater variety of samples. Ensembl’s regulation resources provide a central and easy-to-query repository for reference epigenomes. As with all Ensembl data, it is freely available at http://www.ensembl.org, from the Perl and REST APIs and from the public Ensembl MySQL database server at ensembldb.ensembl.org. Database URL: http://www.ensembl.org
Subfields: Molecular Biology
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In Molecular Biology
- Fiona Cunningham
- Laurent Gil
- Anja Thormann
- Leo Gordon
- S. Searle
- Daniel Barrell
- Doron Lancet
- Benjamin L. Moore
Citations in the corpus
- GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, background): “A confounding factor is that Ensembl and ENCODE invoke two enhancer types, distal and proximal, the latter also identified as ‘pro-moter flanks’ and representing potential promoters (19, 70).”
- Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, background): “Other Ensembl databases specialise in variation and phenotype data (2); whole genome alignments and other comparative genomics information (3); and epigenomic data and regulatory annotation (4).”
- Ensembl 2018 (2017, background): “International epigenomic surveys, including ENCODE Nucleic Acids Research, 2018, Vol. 46, Database issue D755 (10) and Blueprint (11), provided supporting evidence for our genome-wide annotation of regulatory elements (12).”