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Ensembl Regulatory Build specifications

Information


Unique identifier OMICS_19004
Name Ensembl Regulatory Build
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Daniel R. Zerbino
  • person_outline Paul Flicek

Publication for Ensembl Regulatory Build

Ensembl Regulatory Build citations

 (12)
library_books

Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

2018
Nat Commun
PMCID: 5906695
PMID: 29670109
DOI: 10.1038/s41467-018-03828-2

[…] s). Constitutive TFBSs are defined as TFBSs with Ptfbs > 0.75, where Ptfbs is the probability that the TFBS is bound by a TF for any given ENCODE cell line. Ptfbs for all TFBSs were obtained from the ENSEMBL regulatory build. Conserved elements generated by GERP from the alignment of hg19 to 36 mammals were downloaded from the UCSC genome browser.The expected fraction of hotspot (or non-hotspot) m […]

library_books

Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

2017
Nat Commun
PMCID: 5559603
PMID: 28814792
DOI: 10.1038/s41467-017-00366-1

[…] were enriched within specific annotation categories. Annotation information used by fgwas was derived from CADD variant consequence annotation (14 annotations) and monocyte-specific annotations from Ensembl Regulatory build (6 annotations). To identify the set of annotations that would best fit the model, we first tested each of the 20 annotations in a joint data set of reQTLs and ceQTLs includin […]

library_books

Genome annotation for clinical genomic diagnostics: strengths and weaknesses

2017
Genome Med
PMCID: 5448149
PMID: 28558813
DOI: 10.1186/s13073-017-0441-1

[…] example, enhancers) [] and non-coding RNAs (ncRNAs). Large collaborative initiatives, such as ENCODE [] and RoadMap Epigenomics [], have been tasked to create comprehensive maps of these regions. The Ensembl regulatory build [] and Variant Effect Predictor (VEP) [] are able to determine whether variants fall within such regions, but are not yet able to determine pathogenicity, although tools that […]

library_books

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

2016
Cell Stem Cell
PMCID: 5145815
PMID: 27867036
DOI: 10.1016/j.stem.2016.10.019

[…] equencing reads were aligned with Bismark v0.12.2 () and processed with RnBeads v1.5 () to aggregate DNA methylation values on regulatory regions annotated by the August 2015 release of the BLUEPRINT Ensembl Regulatory Build (). Elastic net-regularized general linear models implemented in the R package glmnet () were used for cell-type prediction, and the cell-type similarity graph (F) was derived […]

library_books

Lineage Specific Genome Architecture Links Enhancers and Non coding Disease Variants to Target Gene Promoters

2016
Cell
PMCID: 5123897
PMID: 27863249
DOI: 10.1016/j.cell.2016.09.037

[…] plied to all BLUEPRINT samples with full reference epigenome histone modification alignment files, using default settings and defining 25 epigenetic states. This dataset was used as the basis for the Ensembl Regulatory Build process (), defining regulatory features based on the histone profiles (transcription start site, proximal enhancer, distal enhancer), and also assigning activity statuses bas […]

library_books

ncRNA orthologies in the vertebrate lineage

2016
PMCID: 4792531
PMID: 26980512
DOI: 10.1093/database/bav127

[…] ns are mapped to Rfam entries. tRNAs in the mitochondrial genome are annotated using tRNAscan-SE (). Human and mouse lincRNAs are annotated using cDNA alignments and chromatin-state map data from the Ensembl regulatory build following a similar strategy as described in Guttman et al (). Briefly, regions of chromatin methylation (H3K4me3 and H3K36me3) outside known protein-coding loci are identifie […]

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Ensembl Regulatory Build institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Ensembl Regulatory Build funding source(s)
Supported by the Wellcome Trust (grant number WT095908), the National Human Genome Research Institute (1U01 HG004695, 5U01HG004695), the Biotechnology and Biological Sciences Research Council (BB/I025360/2), the European Molecular Biology Laboratory, the European Union's Seventh Framework Programme (FP7/ 2007-2013) under grant agreement number 282510 (BLUEPRINT), the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement number 223210 (CISSTEM), the European Commission through grant agreement number 018883 (HEROIC), an Integrated Project funded under the 6th Framework Program and by the European Commission under grant agreement number 226073 (SLING), an Integrating Activity within Research Infrastructures of the FP7 Capacities Specific Programm.

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