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ORegAnno specifications

Information


Unique identifier OMICS_07058
Name ORegAnno
Alternative name Open REGulatory ANNOtation database
Restrictions to use None
Data access File download, Browse
Version 3.0
Maintained No

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Publications for Open REGulatory ANNOtation database

ORegAnno citations

 (29)
library_books

Exploring digenic inheritance in arrhythmogenic cardiomyopathy

2017
BMC Med Genet
PMCID: 5723071
PMID: 29221435
DOI: 10.1186/s12881-017-0503-7

[…] idence of at least 0.7. The union of PKP2 interactors from the two databases was selected. (iii) The two gene products are transcription factor and target gene. The Ensembl database [] version 84 and ORegAnno database [] (release 2015.12.22) were manually reviewed for transcription factors of PKP2. (iv) The two gene products participate in the same pathway. “Biological process” (BP) gene annotatio […]

library_books

Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome

2017
Mol Biol Evol
PMCID: 5850737
PMID: 28482049
DOI: 10.1093/molbev/msx154

[…] on defined by inequality”. Physical interactions included those annotated as “direct interaction”, “association”, or “physical association”. We extracted transcription factor–target interactions from ORegAnno (accessed Dec 22, 2015; ), retaining only interacting pairs where the ENSEMBL gene identifier were provided for both genes in order to avoid ambiguity. […]

library_books

Identification of miRNAs Potentially Involved in Bronchiolitis Obliterans Syndrome: A Computational Study

2016
PLoS One
PMCID: 5001701
PMID: 27564214
DOI: 10.1371/journal.pone.0161771

[…] Is provided by TargetMine []. For a given gene, the “Upstream Transcription Factors Template Query” (Targetmine) enables the retrieval of all upstream regulatory genes (TFs) from the AMADEUS [][] and ORegAnno [] libraries of transcription factors-target gene relations. By applying this computational step, each pathway considered was extended to systematically include the TFs for all the genes invo […]

library_books

Feature co localization landscape of the human genome

2016
Sci Rep
PMCID: 4745063
PMID: 26854351
DOI: 10.1038/srep20650

[…] s form blue squares indicating positive co-localizations with one another. The inclusion of TFBS, together with the stronger co-localizations formed by Group I features with the regulatory regions in ORegAnno database (REG), regulatory elements isolated with formaldehyde assistance (FAIRE) and histone-3 lysine-4 trimethylation sites (H3K4) compared to genic sequences in RefSeqGene (GENE) indicate […]

library_books

Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

2015
Genome Biol Evol
PMCID: 4700959
PMID: 26590212
DOI: 10.1093/gbe/evv228

[…] ncluding coding sequences, phylogenetically conserved regions of the genome (phastCons elements), regulatory elements gained or lost in the human lineage, transcription factor binding sites and other oRegAnno regulatory elements, small noncoding RNAs, lincRNAs, disease-associated genes, and candidate SNPs from GWAS studies (see Methods). The results of these enrichment tests are shown in supplemen […]

library_books

Novel therapeutics for coronary artery disease from genome wide association study data

2015
BMC Med Genomics
PMCID: 4460746
PMID: 26044129
DOI: 10.1186/1755-8794-8-S2-S1

[…] rches for genes in the susceptibility genetic loci that bind with common transcription factors. Regulatory information for genes of the search space was retrieved from the Open REGulatory ANNOtation (oRegAnno) database, a publically available database of curated known regulatory elements from the scientific literature []. The MIR module is based on the assumption that dysfunction of micro-RNAs (mi […]

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ORegAnno institution(s)
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA; Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada; Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada; Department of Pathology, Stanford University School of Medicine, Stanford, CA USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
ORegAnno funding source(s)
American Cancer Society [IRG-58-010-58]; Edward Mallinckrodt, Jr. Foundation; National Institutes of Health [K99HG007940, R01HG008150, R01MH101814, K22CA188163]

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