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
Literature & Tutorials:
This record last updated: 02-22-2008