Ensembl regulation resources

Database : the Journal of Biological Databases and Curation
Daniel R ZerbinoP Flicek

Abstract

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.

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Citations

Jun 25, 2016·Database : the Journal of Biological Databases and Curation·Bronwen L AkenStephen M J Searle
Nov 1, 2016·Nature Reviews. Genetics·Jonathan M Mudge, Jennifer Harrow
Dec 3, 2016·Nucleic Acids Research·Bronwen L AkenPaul Flicek
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Nov 21, 2017·Nucleic Acids Research·Daniel R ZerbinoPaul Flicek
Sep 29, 2018·Epigenetics : Official Journal of the DNA Methylation Society·Yunzhang WangSara Hägg
Dec 24, 2018·Database : the Journal of Biological Databases and Curation·Sarah E HuntFiona Cunningham
Oct 29, 2019·Cytogenetic and Genome Research·Alexander KalmbachNuria C Bramswig
Aug 14, 2020·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Timothy ReynoldsElissa J Chesler
Jun 13, 2017·Database : the Journal of Biological Databases and Curation·Simon FishilevichDana Cohen
Jun 16, 2017·Epigenomics·Vinita V KhotSadhana R Joshi
Nov 9, 2018·Nucleic Acids Research·Fiona CunninghamPaul Flicek
Apr 4, 2017·Database : the Journal of Biological Databases and Curation·Magali RuffierPaul Flicek
Nov 3, 2020·Nucleic Acids Research·Kevin L HowePaul Flicek
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May 23, 2017·Trends in Genetics : TIG·Marc S Halfon
Aug 15, 2021·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·David W SantKaren Eilbeck

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
immunoprecipitation
ChIP
ChIP-seq
Bisulfite Sequencing
SELEX

Software Mentioned

VISTA enhancer browser
DIANA
MySQL
Perl Application Programming Interface MySQL
Ensembl Regulatory Build
JASPAR
REST
BioMart
ChromHMM
MultiCell

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