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. 2016 Jan 4;44(D1):D126-32.
doi: 10.1093/nar/gkv1203. Epub 2015 Nov 17.

ORegAnno 3.0: A Community-Driven Resource for Curated Regulatory Annotation

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Free PMC article

ORegAnno 3.0: A Community-Driven Resource for Curated Regulatory Annotation

Robert Lesurf et al. Nucleic Acids Res. .
Free PMC article

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/.

Figures

Figure 1.
Figure 1.
Current content of the ORegAnno database. Content statistics are divided by species (A and B), regulatory type (C and D), and data source (E and F).
Figure 2.
Figure 2.
Comparison of the genomic coverage captured by ORegAnno and the ENSEMBL Regulatory Track. A Venn diagram demonstrates coverage overlaps for human genome assembly version GRCh38/hg38, with sets sized to scale. The ENSEMBL Regulatory Track is divided into two main sets, a track overview set and the transcription factor binding site (TFBS) set.
Figure 3.
Figure 3.
Capture reagent using ORegAnno sites improves coverage of regulatory regions in human hepatocellular carcinoma. (A) Coverage across the entire ‘regulome’ is visualized as a heatmap for each of the ten HCC cases. WRS samples have greater sequencing read depth across the targeted region, compared with WGS samples. (B) An illustrative IGV (51) screenshot is shown of the TERT promoter for one HCC case. A canonical C228T somatic mutation is observed in the WRS data, but cannot be reliably called in the WGS data.

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References

    1. Montgomery S.B., Griffith O.L., Sleumer M.C., Bergman C.M., Bilenky M., Pleasance E.D., Prychyna Y., Zhang X., Jones S.J. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics. 2006;22:637–640. - PubMed
    1. Griffith O.L., Montgomery S.B., Bernier B., Chu B., Kasaian K., Aerts S., Mahony S., Sleumer M.C., Bilenky M., Haeussler M., et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 2008;36:D107–D113. - PMC - PubMed
    1. The Encode Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74. - PMC - PubMed
    1. Doolittle W.F. Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. U.S.A. 2013;110:5294–5300. - PMC - PubMed
    1. Eddy S.R. The ENCODE project: missteps overshadowing a success. Curr. Biol. 2013;23:R259–261. - PubMed

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