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ORegAnno 3.0: a community-driven resource for curated regulatory annotation

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Lesurf, Robert, Cotto, Kelsy C., Wang, Grace, Griffith, Malachi, Kasaian, Katayoon, Jones, Steven J. M., Montgomery, Stephen B., Griffith, Obi L. +1 more·2016·Nucleic Acids Research
DOI 10.1093/nar/gkv1203PMC PMC4702855
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Abstract

The Open Regulatory Annotation database (ORegAnno) is a resource for curated regulatory annotation. It contains information about regulatory regions, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, and other regulatory elements. ORegAnno differentiates itself from other regulatory resources by facilitating crowd-sourced interpretation and annotation of regulatory observations from the literature and highly curated resources. It contains a comprehensive annotation scheme that aims to describe both the elements and outcomes of regulatory events. Moreover, ORegAnno assembles these disparate data sources and annotations into a single, high quality catalogue of curated regulatory information. The current release is an update of the database previously featured in the NAR Database Issue, and now contains 1 948 307 records, across 18 species, with a combined coverage of 334 215 080 bp. Complete records, annotation, and other associated data are available for browsing and download at http://www.oreganno.org/.

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  • DMR_394 overlaps known regulatory and transcription factor binding sites from the Open Regulatory Annotation Database.

    “Consistently, we found this DMR to overlap known regulatory and transcription factor binding sites from the Open Regulatory Annotation Database28.”

    From Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice (2021) · cites this paper as [28]

  • The putative role of the human orthologous region as a hippocampal regulatory element is conserved in human.

    “Furthermore, several CTCF binding sites were reported at this region28 suggesting the putative role of this region as a hippocampal regulatory element is conserved in human (Fig. 6B).”

    From Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice (2021) · cites this paper as [28]

    The citation is attached to the report of several CTCF binding sites at this region; the proposed conserved hippocampal role is the citing authors’ inference. Our copy’s Results discuss curated regulatory annotations generally, but neither those passages nor searches for CTCF binding sites and hippocampal conservation identify binding sites at this particular region. The cited paper therefore does not verify the region-specific report in the citing sentence. (LLM, conf=0.73)

    Experimental — accuracy not yet measured

  • Several CTCF binding sites were reported at the human orthologous region.

    “Furthermore, several CTCF binding sites were reported at this region28”

    From Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice (2021) · cites this paper as [28]

    The Results sections on New records and Applications describe curated transcription-factor binding sites generally, but do not identify CTCF sites at the human orthologous region. Searches for “CTCF” and “CTCF binding sites human orthologous region” found no passage addressing that specific claim. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Lesurf, R., Cotto, K. C., Wang, G., Griffith, M., Kasaian, K., Jones, S. J. M., Montgomery, S. B., Griffith, O. L., & The Open Regulatory Annotation Consortium
Affiliations
  • Washington University in St. Louis (US)
  • BC Cancer Agency (CA)
  • Stanford Medicine (US)
Corresponding author
Griffith, Obi L.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2015-11-17
Volume
44
Issue
D1
Pages
D126-D132
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkv1203
PMC
PMC4702855
OpenAlex
W2188035077
Cited by
201
References
4
Citations by year
2026: 7 · 2025: 19 · 2024: 32 · 2023: 21 · 2022: 26 · 2021: 31 · 2020: 24 · 2019: 16 · 2018: 11 · 2017: 8 · 2016: 4
FWCI
3.48
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
  • HighWire Press Open Archive (submittedVersion)
Funders
  • National Institute of Mental Health (R01MH101814)
  • National Human Genome Research Institute (R01HG008150, K99HG007940)
  • National Cancer Institute (K22CA188163)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
Keywords
regulatory annotation, regulatory elements, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, crowdsourced annotation, curated database, annotation scheme
MeSH terms
Binding Sites, Regulatory Sequences, Nucleic Acid, RNA, Transcription Factors, Databases, Nucleic Acid, Molecular Sequence Annotation

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