ORegAnno -- an open-access community-driven resource for regulatory annotation

What you can do:
Find experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants using this open-source, open-access database and literature curation system for community-based annotation.
Highlights:
  • The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species.
  • A new feature called the 'publication queue' allows users to input relevant papers from scientific literature as targets for annotation.
  • The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods.
  • Users can enter or 'check out' papers from the queue for manual curation using a series of user-friendly annotation pages.
  • A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence.
  • An evidence ontology was developed to describe and categorize these experiments.
  • Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers.
Keywords:
  • DNA regulatory regions
  • transcription factor binding sites
  • regulatory variants
  • regulatory sequence
  • regulatory annotation
  • text mining
  • manual curation
  • open source
This record last updated: 02-22-2008
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