Note: lifted from sacCer1
Description
This track displays literature-curated regulatory regions, transcription
factor binding sites, and regulatory polymorphisms from
ORegAnno (Open Regulatory Annotation). For more detailed
information on a particular regulatory element, follow the link to ORegAnno
from the details page.
Display Conventions and Configuration
The display may be filtered to show only selected region types, such as:
- regulatory regions (shown in light blue)
- regulatory polymorphisms (shown in dark blue)
- transcription factor binding sites (shown in orange)
- regulatory haplotypes (shown in red)
- miRNA binding sites (shown in blue-green)
To exclude a region type, uncheck the appropriate box in the list at the top of
the Track Settings page.
Methods
An ORegAnno record describes an experimentally proven and published regulatory
region (promoter, enhancer, etc.), transcription factor binding site, or
regulatory polymorphism. Each annotation must have the following attributes:
- A stable ORegAnno identifier.
- A valid taxonomy ID from the NCBI taxonomy database.
- A valid PubMed reference.
- A target gene that is either user-defined, in Entrez Gene or in EnsEMBL.
- A sequence with at least 40 flanking bases (preferably more) to allow the
site to be mapped to any release of an associated genome.
- At least one piece of specific experimental evidence, including the
biological technique used to discover the regulatory sequence. (Currently
only the evidence subtypes are supplied with the UCSC track.)
- A positive, neutral or negative outcome based on the experimental results
from the primary reference. (Only records with a positive outcome are currently
included in the UCSC track.)
The following attributes are optionally included:
- A transcription factor that is either user-defined, in Entrez Gene
or in EnsEMBL.
- A specific cell type for each piece of experimental evidence, using the
eVOC cell type ontology.
- A specific dataset identifier (e.g. the REDfly dataset) that allows
external curators to manage particular annotation sets using ORegAnno's
curation tools.
- A "search space" sequence that specifies the region that was
assayed, not just the regulatory sequence.
- A dbSNP identifier and type of variant (germline, somatic or artificial)
for regulatory polymorphisms.
Mapping to genome coordinates is performed periodically to current genome
builds by BLAST sequence alignment.
The information provided in this track represents an abbreviated summary of the
details for each ORegAnno record. Please visit the official ORegAnno entry
(by clicking on the ORegAnno link on the details page of a specific regulatory
element) for complete details such as evidence descriptions, comments,
validation score history, etc.
Credits
ORegAnno core team and principal contacts: Stephen Montgomery, Obi Griffith,
and Steven Jones from Canada's Michael Smith Genome Sciences Centre, Vancouver,
British Columbia, Canada.
The ORegAnno community (please see individual citations for various
features): ORegAnno Citation.
References
Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open
Regulatory Annotation Consortium..
ORegAnno 3.0: a community-driven resource for curated regulatory annotation.
Nucleic Acids Res. 2016 Jan 4;44(D1):D126-32.
PMID: 26578589; PMC: PMC4702855
Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M,
Haeussler M et al.
ORegAnno: an open-access community-driven resource for regulatory annotation.
Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13.
PMID: 18006570; PMC: PMC2239002
Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED,
Prychyna Y, Zhang X, Jones SJ.
ORegAnno: an open access database and curation system for
literature-derived promoters, transcription factor binding sites and regulatory variation.
Bioinformatics. 2006 Mar 1;22(5):637-40.
PMID: 16397004
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