Open Regulatory Annotation
Names
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Open Regulatory Annotation
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ORegAnno
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
Open regulatory annotation database
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
oreganno
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
Names
More detailed information about this field from each metasource.
Open Regulatory Annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ORegAnno
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
Open regulatory annotation database
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
oreganno
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.869309
Other names: ORegAnno, Open regulatory annotation database, oreganno
Names
More detailed information about this field from each metasource.
Open Regulatory Annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ORegAnno
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
Open regulatory annotation database
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
oreganno
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.869309
The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database.
Description
More detailed information about this field from each metasource.
The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database.
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Open REGulatory ANNOtation database
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
>>>!!!<<< 2017-06-02: We recently suffered a server failure and are working to bring the full ORegAnno website back online. In the meantime, you may download the complete database here: http://www.oreganno.org/dump/ ; Data are also available through UCSC Genome Browser (e.g., hg38 -> Regulation -> ORegAnno) https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=686342163_2it3aVMQVoXWn0wuCjkNOVX39wxy&c=chr1&g=oreganno >>>!!!<<< The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes.
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
Collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.869309
Webpage:
http://www.oreganno.org/Webpage
More detailed information about this field from each metasource.
http://www.oreganno.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
Licence:
Name: otherLicence name
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other
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
Licence URL
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https://www.gnu.org/copyleft/lesser.html
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
Publications:
Publications
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ORegAnno: an open-access community-driven resource for regulatory annotation
PMID: 18006570
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
PMID: 16397004
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
Publications
More detailed information about this field from each metasource.
ORegAnno: an open-access community-driven resource for regulatory annotation
PMID: 18006570
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
PMID: 16397004
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
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ORegAnno: an open-access community-driven resource for regulatory annotation
PubMed citations: 142.
142 articles citing: ORegAnno: an open-access community-driven resource for regulatory annotation
Expression variations in ectodysplasin-A gene (eda) may contribute to morphological divergence of scales in haplochromine cichlids. PMID:35272610
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PMID:34665801
Many chronological aging clocks can be found throughout the epigenome: Implications for quantifying biological aging. PMID:34655509
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants. PMID:34021560
Role of Myc Proto-Oncogene as a Transcriptional Hub to Regulate the Expression of Regeneration-Associated Genes following Preconditioning Peripheral Nerve Injury. PMID:33262248
HAHmiR.DB: a server platform for high-altitude human miRNA-gene coregulatory networks and associated regulatory circuits. PMID:33259604
LRRK2 mediates microglial neurotoxicity via NFATc2 in rodent models of synucleinopathies. PMID:33055242
Critical Analysis of Genome-Wide Association Studies: Triple Negative Breast Cancer Quae Exempli Causa. PMID:32823908
Signature-based approaches for informed drug repurposing: targeting CNS disorders. PMID:32604402
Subacute cannabidiol alters genome-wide DNA methylation in adult mouse hippocampus. PMID:32579259
Mapping and characterization of structural variation in 17,795 human genomes. PMID:32460305
The TargetMine Data Warehouse: Enhancement and Updates. PMID:31649722
Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis-Regulatory Code. PMID:31356126
Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma. PMID:31215230
Myometrial Transcriptional Signatures of Human Parturition. PMID:30988671
Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer. PMID:30934003
The rs61742690 (S783N) single nucleotide polymorphism is a suitable target for disrupting BCL11A-mediated foetal-to-adult globin switching. PMID:30768627
In silico approach to identify non-synonymous SNPs with highest predicted deleterious effect on protein function in human obesity related gene, neuronal growth regulator 1 (NEGR1). PMID:30402368
Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing. PMID:30245013
Epigenome-Wide Analyses Identify Two Novel Associations With Recurrent Stroke in the Vitamin Intervention for Stroke Prevention Clinical Trial. PMID:30237808
No Evidence for Recent Selection at FOXP2 among Diverse Human Populations. PMID:30078708
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Identifying noncoding risk variants using disease-relevant gene regulatory networks. PMID:29453388
Fourteen sequence variants that associate with multiple sclerosis discovered by meta-analysis informed by genetic correlations. PMID:29263835
A causal mediation model of ischemia reperfusion injury in the retina. PMID:29121052
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PMID:28949986
The Genetic Origin of Short Tail in Endangered Korean Dog, DongGyeongi. PMID:28855671
COGNATE: comparative gene annotation characterizer. PMID:28716078
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. PMID:27922122
Interferons Induce Expression of SAMHD1 in Monocytes through Down-regulation of miR-181a and miR-30a. PMID:27909056
Evaluating tools for transcription factor binding site prediction. PMID:27806697
Cross-species Conservation of context-specific networks. PMID:27531214
DL-ADR: a novel deep learning model for classifying genomic variants into adverse drug reactions. PMID:27510822
Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis. PMID:27295045
Predicting regulatory variants with composite statistic. PMID:27273672
Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila. PMID:27247329
rAAV-compatible MiniPromoters for restricted expression in the brain and eye. PMID:27164903
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. PMID:27118214
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity. PMID:27056836
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Association of the IGF1 gene with fasting insulin levels. PMID:26860063
Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor. PMID:26715627
Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain. PMID:26590212
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. PMID:26586797
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. PMID:26578589
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Paired exome analysis of Barrett's esophagus and adenocarcinoma. PMID:26192918
Novel therapeutics for coronary artery disease from genome-wide association study data. PMID:26044129
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. PMID:26013488
TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. PMID:25943543
Genome-wide identification of microRNA expression quantitative trait loci. PMID:25791433
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. PMID:25725063
Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PMID:25679813
Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. PMID:25635527
Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs. PMID:25618141
Type I diabetes mellitus: genetic factors and presumptive enteroviral etiology or protection. PMID:25574400
GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. PMID:25428361
Distinct roles for histone chaperones in the deposition of Htz1 in chromatin. PMID:25338502
Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells. PMID:25080971
Strategies to design and analyze targeted sequencing data: cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. PMID:24951659
GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. PMID:24931982
Functional annotation signatures of disease susceptibility loci improve SNP association analysis. PMID:24886216
Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer. PMID:24786295
Determining causality and consequence of expression quantitative trait loci. PMID:24770875
Large-scale analysis of tandem repeat variability in the human genome. PMID:24682812
Dissecting the causal genetic mechanisms of coronary heart disease. PMID:24623178
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease. PMID:24498628
RANK- and c-Met-mediated signal network promotes prostate cancer metastatic colonization. PMID:24478054
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development. PMID:24378202
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria. PMID:24234444
Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner. PMID:24204606
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. PMID:24156763
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. PMID:23981286
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. PMID:23770607
Detection and impact of rare regulatory variants in human disease. PMID:23755067
GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. PMID:23723249
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. PMID:23710289
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. PMID:23547897
Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. PMID:23525077
LASAGNA: a novel algorithm for transcription factor binding site alignment. PMID:23522376
Using BioBin to explore rare variant population stratification. PMID:23424138
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
Patterns of methylation heritability in a genome-wide analysis of four brain regions. PMID:23303775
Chapter 11: Genome-wide association studies. PMID:23300413
An integrative approach to inferring gene regulatory module networks. PMID:23285197
Histone demethylase Jumonji D3 (JMJD3) as a tumor suppressor by regulating p53 protein nuclear stabilization. PMID:23236496
HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. PMID:22900683
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. PMID:22610119
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PMID:22412381
Transcription factor binding site redundancy in embryonic enhancers of the Drosophila bithorax complex. PMID:22384371
Fast, sensitive discovery of conserved genome-wide motifs. PMID:22300316
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. PMID:22208852
Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. PMID:22178994
Semantic annotation of biological concepts interplaying microbial cellular responses. PMID:22122862
The chromosome 2p21 region harbors a complex genetic architecture for association with risk for renal cell carcinoma. PMID:22113997
Identification of cis-regulatory sequence variations in individual genome sequences. PMID:21989199
Silencing of p130cas in ovarian carcinoma: a novel mechanism for tumor cell death. PMID:21957230
The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. PMID:21884625
Lrig1 is an estrogen-regulated growth suppressor and correlates with longer relapse-free survival in ERα-positive breast cancer. PMID:21821674
Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs. PMID:21821017
The mutational landscape of head and neck squamous cell carcinoma. PMID:21798893
Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. PMID:21787409
Identifying functional single nucleotide polymorphisms in the human CArGome. PMID:21771879
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome. PMID:21602498
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PMID:21408081
Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. PMID:21190561
Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. PMID:21177970
Genetic factors and diet affect long-bone length in the F34 LG,SM advanced intercross. PMID:21170743
Patterns of human gene expression variance show strong associations with signaling network hierarchy. PMID:21073694
Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. PMID:21059887
Transcriptional regulation of mammalian miRNA genes. PMID:20977933
Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PMID:20808879
Identification of hookworm DAF-16/FOXO response elements and direct gene targets. PMID:20808816
Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. PMID:20668662
PriorsEditor: a tool for the creation and use of positional priors in motif discovery. PMID:20628076
Biomedical semantics: the hub for biomedical research 2.0. PMID:20618983
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. PMID:20478823
Most transcription factor binding sites are in a few mosaic classes of the human genome. PMID:20459624
Semantic integration of data on transcriptional regulation. PMID:20427517
Comprehensive mapping of the human kinome to epidermal growth factor receptor signaling. PMID:20421302
LINNAEUS: a species name identification system for biomedical literature. PMID:20149233
Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. PMID:20100800
An effective tri-clustering algorithm combining expression data with gene regulation information. PMID:19838334
Enhancing navigation in biomedical databases by community voting and database-driven text classification. PMID:19799796
A protein-protein interaction guided method for competitive transcription factor binding improves target predictions. PMID:19786498
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. PMID:19704032
myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks. PMID:19500400
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. PMID:19374773
Integrating sequence, evolution and functional genomics in regulatory genomics. PMID:19226437
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. PMID:19151087
The UCSC Genome Browser Database: update 2009. PMID:18996895
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. PMID:18453628
Text-mining assisted regulatory annotation. PMID:18271954 -
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
PubMed citations: 67.
67 articles citing: ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
A novel network based linear model for prioritization of synergistic drug combinations. PMID:35381038
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PMID:34665801
A chromatin-associated splicing isoform of OIP5-AS1 acts in cis to regulate the OIP5 oncogene. PMID:33404283
CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs. PMID:31797625
Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer. PMID:30934003
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. PMID:30727967
A map of direct TF-DNA interactions in the human genome. PMID:30517703
Epigenome-Wide Analyses Identify Two Novel Associations With Recurrent Stroke in the Vitamin Intervention for Stroke Prevention Clinical Trial. PMID:30237808
No Evidence for Recent Selection at FOXP2 among Diverse Human Populations. PMID:30078708
Landscape of transcriptional deregulation in lung cancer. PMID:29866045
Interferons Induce Expression of SAMHD1 in Monocytes through Down-regulation of miR-181a and miR-30a. PMID:27909056
Evaluating tools for transcription factor binding site prediction. PMID:27806697
Identification of miRNAs Potentially Involved in Bronchiolitis Obliterans Syndrome: A Computational Study. PMID:27564214
rAAV-compatible MiniPromoters for restricted expression in the brain and eye. PMID:27164903
Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain. PMID:26590212
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. PMID:26578589
Identification of Biomarker and Co-Regulatory Motifs in Lung Adenocarcinoma Based on Differential Interactions. PMID:26402252
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
Compound hierarchical correlated beta mixture with an application to cluster mouse transcription factor DNA binding data. PMID:25964663
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. PMID:25925574
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. PMID:25865119
PDYN, a gene implicated in brain/mental disorders, is targeted by REST in the adult human brain. PMID:25220237
Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. PMID:24973796
Functional annotation signatures of disease susceptibility loci improve SNP association analysis. PMID:24886216
Dissecting the causal genetic mechanisms of coronary heart disease. PMID:24623178
Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer. PMID:24200043
Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. PMID:23770607
A systems approach to rheumatoid arthritis. PMID:23240033
Histone demethylase Jumonji D3 (JMJD3) as a tumor suppressor by regulating p53 protein nuclear stabilization. PMID:23236496
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. PMID:22839973
Fast, sensitive discovery of conserved genome-wide motifs. PMID:22300316
Dissecting the regulatory architecture of gene expression QTLs. PMID:22293038
Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. PMID:21787409
Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. PMID:21190561
Genetic factors and diet affect long-bone length in the F34 LG,SM advanced intercross. PMID:21170743
Theoretical and empirical quality assessment of transcription factor-binding motifs. PMID:20923783
is-rSNP: a novel technique for in silico regulatory SNP detection. PMID:20823317
The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. PMID:20647237
MER41 repeat sequences contain inducible STAT1 binding sites. PMID:20625510
Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. PMID:20215436
A population genetic hidden Markov model for detecting genomic regions under selection. PMID:20185453
Comparative analyses of single-nucleotide polymorphisms in the TNF promoter region provide further validation for the vervet monkey model of obesity. PMID:20034434
MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. PMID:19409082
Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. PMID:19383880
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. PMID:18971253
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PMID:18927605
Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. PMID:18793454
Low nucleosome occupancy is encoded around functional human transcription factor binding sites. PMID:18627598
Identification of a set of genes showing regionally enriched expression in the mouse brain. PMID:18625066
Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. PMID:18611952
In silico regulatory analysis for exploring human disease progression. PMID:18564415
Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes. PMID:18547402
CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. PMID:18535663
Identification of transcription factor contexts in literature using machine learning approaches. PMID:18426546
Probabilistic inference of transcription factor binding from multiple data sources. PMID:18364997
SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. PMID:18315851
Text-mining assisted regulatory annotation. PMID:18271954
In silico detection of sequence variations modifying transcriptional regulation. PMID:18208319
The UCSC Genome Browser Database: 2008 update. PMID:18086701
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. PMID:18039705
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. PMID:18006571
ORegAnno: an open-access community-driven resource for regulatory annotation. PMID:18006570
Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PMID:17973026
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. PMID:17916232
A survey of genomic properties for the detection of regulatory polymorphisms. PMID:17559298
EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. PMID:17233892
Practical strategies for discovering regulatory DNA sequence motifs. PMID:16683017
Tags:
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
c. elegans
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
drosophila melanogaster
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
saccharomyces
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
gallus gallus
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
human
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
rat
metasource: re3data.org
version: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
genetic variation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
gene regulation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.869309
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: ORegAnno; Open Regulatory Annotation; DOI: https://doi.org/10.25504/FAIRsharing.8dak0r; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
c. elegans
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
drosophila melanogaster
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
saccharomyces
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
gallus gallus
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
human
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
rat
metasource: re3data.orgversion: re3data.org: ORegAnno; editing status 2019-11-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DG70 last accessed: 2022-11-04
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.869309
genetic variation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.869309
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.869309
gene regulation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.869309
biological regulation gene protein small molecule nucleic acid sequence transcription c. elegans drosophila melanogaster saccharomyces gallus gallus human rat transcription factors and regulatory sites genetic variation gene expression gene regulation
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