Schema for ORegAnno - Regulatory elements from ORegAnno
  Database: sacCer3    Primary Table: oreganno    Row Count: 7,299   Data last updated: 2016-04-28
Format description: track for regulatory regions from ORegAnno
fieldexampleSQL type info description
bin 585smallint(5) unsigned range A field to speed indexing
chrom chrIvarchar(255) values Chromosome
chromStart 45027int(10) unsigned range Start position in chrom
chromEnd 45875int(10) unsigned range End position in chrom
id OREG0037954varchar(48) values unique ID to identify this regulatory region
strand +char(1) values + or -
name OREG0037954varchar(255) values name of regulatory region

Connected Tables and Joining Fields
        sacCer3.oregannoAttr.id (via oreganno.id)
      sacCer3.oregannoLink.id (via oreganno.id)

Sample Rows
 
binchromchromStartchromEndidstrandname
585chrI4502745875OREG0037954+OREG0037954
585chrI4502745875OREG0037822+OREG0037822
585chrI4502745875OREG0037718+OREG0037718
585chrI4514145152OREG0027043-OREG0027043
585chrI4523945250OREG0027044+OREG0027044
585chrI4531745332OREG0026892-OREG0026892
585chrI4547945488OREG0026773+OREG0026773
585chrI4549745512OREG0026893-OREG0026893
585chrI5848458700OREG0038017+OREG0038017
585chrI5853758548OREG0027115+OREG0027115

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

ORegAnno (oreganno) Track Description
 

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