Regulatory Element Database for Drosophila
Names
More detailed information about this field from each metasource.
Regulatory Element Database for Drosophila
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
REDfly
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
redfly
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
Names
More detailed information about this field from each metasource.
Regulatory Element Database for Drosophila
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
REDfly
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
redfly
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
Names
More detailed information about this field from each metasource.
Regulatory Element Database for Drosophila
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
REDfly
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
redfly
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence, their associated genes, and the expression patterns they direct.
Description
More detailed information about this field from each metasource.
REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence, their associated genes, and the expression patterns they direct.
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Regulatory modules and transcription factor binding sites in Drosophila
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The REDfly database of Drosophila transcriptional cis-regulatory elements provides experimentally validated cis-regulatory modules and transcription factor binding sites. The user interface is designed for access by both causal and power users and is intended as a tool for facilitating computational as well as experimental studies of transcriptional regulation.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
Webpage:
http://redfly.ccr.buffalo.edu/Webpage
More detailed information about this field from each metasource.
http://redfly.ccr.buffalo.edu/
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://redfly.ccr.buffalo.edu
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
Licence:
Name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by-nc-nd/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
PMID: 20965965
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
PMID: 18039705
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
REDfly: a Regulatory Element Database for Drosophila
PMID: 16303794
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
REDfly: the transcriptional regulatory element database for Drosophila
PMID: 30329093
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Publications
More detailed information about this field from each metasource.
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
PMID: 20965965
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
PMID: 18039705
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
REDfly: a Regulatory Element Database for Drosophila
PMID: 16303794
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
REDfly: the transcriptional regulatory element database for Drosophila
PMID: 30329093
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
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REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
PubMed citations: 115.
115 articles citing: REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. PMID:35886794
Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding. PMID:35465052
Enhancer-silencer transitions in the human genome. PMID:35105669
The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression. PMID:33987532
Enhancer redundancy in development and disease. PMID:33442000
Chromatin Structure and Function in Mosquitoes. PMID:33365050
Shared distal regulatory regions may contribute to the coordinated expression of human ribosomal protein genes. PMID:32240723
Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation. PMID:32080242
Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts. PMID:31704182
Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis-Regulatory Code. PMID:31356126
The Role of Chromatin Accessibility in cis-Regulatory Evolution. PMID:31114856
ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. PMID:30962180
Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. PMID:30598455
Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases. PMID:30553552
CRM Discovery Beyond Model Insects. PMID:30414115
Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis. PMID:30393032
Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic. PMID:30383747
REDfly: the transcriptional regulatory element database for Drosophila. PMID:30329093
Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos. PMID:30192762
Prediction and identification of transcriptional regulatory elements at the lung cancer-specific DKK1 locus. PMID:29928394
Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection. PMID:29850830
Reduced Neuronal Transcription of Escargot, the Drosophila Gene Encoding a Snail-Type Transcription Factor, Promotes Longevity. PMID:29760717
Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo. PMID:29727464
The cis-regulatory dynamics of embryonic development at single-cell resolution. PMID:29539636
The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription. PMID:29378788
Evidence for a hierarchical transcriptional circuit in Drosophila male germline involving testis-specific TAF and two gene-specific transcription factors, Mod and Acj6. PMID:29235675
Hippo, TGF-β, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection. PMID:29108021
McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes. PMID:29070071
The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies. PMID:28982128
Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA. PMID:28978476
GRID-seq reveals the global RNA-chromatin interactome. PMID:28922346
Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network. PMID:28898266
Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. PMID:28792889
Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers. PMID:28589862
Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster. PMID:28584716
Perspectives on Gene Regulatory Network Evolution. PMID:28528721
A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model. PMID:28497059
Creating cell type-specific mutants by enhancer mutagenesis. PMID:28446593
Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements. PMID:28381411
Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression. PMID:28320313
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. PMID:27899608
SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules. PMID:27637070
Maps of context-dependent putative regulatory regions and genomic signal interactions. PMID:27625394
Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks. PMID:27600224
Cross-species Conservation of context-specific networks. PMID:27531214
CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design. PMID:27487245
Redeployment of a conserved gene regulatory network during Aedes aegypti development. PMID:27341759
Chromatin Heterogeneity and Distribution of Regulatory Elements in the Late-Replicating Intercalary Heterochromatin Domains of Drosophila melanogaster Chromosomes. PMID:27300486
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. PMID:26998229
The Capacity to Act in Trans Varies Among Drosophila Enhancers. PMID:26984057
Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states. PMID:26841971
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. PMID:26586237
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. PMID:26578589
Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PMID:26505748
MEPD: medaka expression pattern database, genes and more. PMID:26450962
TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos. PMID:26381166
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. PMID:26335633
Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster. PMID:26129990
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
Regulation of transcription factors on sexual dimorphism of fig wasps. PMID:26031454
Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster. PMID:25933381
Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila. PMID:25887553
Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. PMID:25791631
Identifying transcriptional cis-regulatory modules in animal genomes. PMID:25704908
Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PMID:25679813
cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. PMID:25521507
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. PMID:25442502
Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression. PMID:25349675
Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition. PMID:25313869
Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. PMID:25173756
Enhancer loops appear stable during development and are associated with paused polymerase. PMID:25043061
Integrating the interactome and the transcriptome of Drosophila. PMID:24913703
Genome-scale functional characterization of Drosophila developmental enhancers in vivo. PMID:24896182
SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete. PMID:24886562
Global view of enhancer-promoter interactome in human cells. PMID:24821768
Regulation of gene expression in the genomic context. PMID:24688749
Resources for functional genomics studies in Drosophila melanogaster. PMID:24653003
Quantitative modeling of a gene's expression from its intergenic sequence. PMID:24604095
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data. PMID:24400020
The role of Dichaete in transcriptional regulation during Drosophila embryonic development. PMID:24314314
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. PMID:24271386
A common set of DNA regulatory elements shapes Drosophila appendages. PMID:24229644
The Drosophila anatomy ontology. PMID:24139062
Flanking sequence context-dependent transcription factor binding in early Drosophila development. PMID:24093548
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PMID:24068946
A locus in Drosophila sechellia affecting tolerance of a host plant toxin. PMID:24037270
Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis. PMID:23997651
Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs. PMID:23922708
Messenger RNA is a functional component of a chromatin insulator complex. PMID:23917615
A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. PMID:23873954
Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. PMID:23852450
Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo. PMID:23822503
Drosophila functional elements are embedded in structurally constrained sequences. PMID:23750124
The impact of trans-regulation on the evolutionary rates of metazoan proteins. PMID:23658220
Genome-wide control of RNA polymerase II activity by cohesin. PMID:23555293
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. PMID:23525069
A statistical thin-tail test of predicting regulatory regions in the Drosophila genome. PMID:23409927
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. PMID:23063361
P-value-based regulatory motif discovery using positional weight matrices. PMID:22990209
Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. PMID:22893002
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. PMID:22499593
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PMID:22412381
Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. PMID:22296846
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. PMID:22231485
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. PMID:22208852
Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules. PMID:22115527
Automated protein-DNA interaction screening of Drosophila regulatory elements. PMID:22037703
pubmed2ensembl: a resource for mining the biological literature on genes. PMID:21980353
RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. PMID:21852534
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. PMID:21821659
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. PMID:21672956
Genome Surveyor 2.0: cis-regulatory analysis in Drosophila. PMID:21593125 -
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
PubMed citations: 54.
54 articles citing: REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. PMID:35886794
Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo. PMID:34849867
Chromatin Structure and Function in Mosquitoes. PMID:33365050
Transcriptional Enhancers in Drosophila. PMID:32878914
Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. PMID:30598455
REDfly: the transcriptional regulatory element database for Drosophila. PMID:30329093
Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands. PMID:30005604
FlyExpress 7: An Integrated Discovery Platform To Study Coexpressed Genes Using in Situ Hybridization Images in Drosophila. PMID:28667017
An Enhancer's Length and Composition Are Shaped by Its Regulatory Task. PMID:28588608
Structure of the Transcriptional Regulatory Network Correlates with Regulatory Divergence in Drosophila. PMID:28333240
The Insect Prothoracic Gland as a Model for Steroid Hormone Biosynthesis and Regulation. PMID:27320926
Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks. PMID:26680653
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. PMID:26586237
Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer. PMID:24786295
Temporal regulation of Dpp signaling output in the Drosophila wing. PMID:24591046
MEF2 is an in vivo immune-metabolic switch. PMID:24075010
Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. PMID:23852450
Three enhancements to the inference of statistical protein-DNA potentials. PMID:23042633
Combinatorial control of temporal gene expression in the Drosophila wing by enhancers and core promoters. PMID:22992320
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. PMID:22950945
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. PMID:22456606
CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. PMID:22422836
Evolutionary origins of transcription factor binding site clusters. PMID:22075113
Formation of regulatory modules by local sequence duplication. PMID:21998564
Selection and constraint on regulatory elements in Drosophila simulans. PMID:21904868
The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. PMID:21884625
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. PMID:21821659
MotifClick: prediction of cis-regulatory binding sites via merging cliques. PMID:21679436
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. PMID:21473766
Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. PMID:21187896
Assessing computational methods of cis-regulatory module prediction. PMID:21152003
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. PMID:21097781
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. PMID:21036869
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. PMID:20965965
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PMID:20808951
Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. PMID:20668662
The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. PMID:20647237
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PMID:20351773
Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix. PMID:20339533
Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. PMID:20126523
A comprehensive map of insulator elements for the Drosophila genome. PMID:20084099
A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. PMID:19956545
Combinatorial binding predicts spatio-temporal cis-regulatory activity. PMID:19890324
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. PMID:19853570
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. PMID:19758432
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. PMID:19656951
Organization of developmental enhancers in the Drosophila embryo. PMID:19651877
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. PMID:19633094
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. PMID:19627575
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs. PMID:19284541
Big genomes facilitate the comparative identification of regulatory elements. PMID:19259274
Evolution of regulatory sequences in 12 Drosophila species. PMID:19132088
Microarray transfection analysis of conserved genomic sequences from three immediate early genes. PMID:18955127
PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling. PMID:18769735 -
REDfly: a Regulatory Element Database for Drosophila
PubMed citations: 46.
46 articles citing: REDfly: a Regulatory Element Database for Drosophila
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. PMID:35886794
The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila. PMID:33677563
Chromatin Structure and Function in Mosquitoes. PMID:33365050
Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. PMID:30598455
REDfly: the transcriptional regulatory element database for Drosophila. PMID:30329093
Simple Expression Domains Are Regulated by Discrete CRMs During Drosophila Oogenesis. PMID:28634244
Incorporating chromatin accessibility data into sequence-to-expression modeling. PMID:25762337
TWO-LAYER MATHEMATICAL MODELING OF GENE EXPRESSION: INCORPORATING DNA-LEVEL INFORMATION AND SYSTEM DYNAMICS. PMID:25328249
Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data. PMID:24565409
Response to the BMP gradient requires highly combinatorial inputs from multiple patterning systems in the Drosophila embryo. PMID:22513375
Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers. PMID:22174086
Integrating overlapping structures and background information of words significantly improves biological sequence comparison. PMID:22102867
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. PMID:22058225
Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PMID:22028675
Formation of regulatory modules by local sequence duplication. PMID:21998564
Selection and constraint on regulatory elements in Drosophila simulans. PMID:21904868
The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. PMID:21884625
STAT is an essential activator of the zygotic genome in the early Drosophila embryo. PMID:21637778
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. PMID:20965965
The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. PMID:20647237
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. PMID:20624780
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. PMID:19715598
DISCOVER: a feature-based discriminative method for motif search in complex genomes. PMID:19478006
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution. PMID:19293946
Big genomes facilitate the comparative identification of regulatory elements. PMID:19259274
Compo: composite motif discovery using discrete models. PMID:19063744
PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling. PMID:18769735
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PMID:18584029
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. PMID:18583644
Positive and negative selection on noncoding DNA in Drosophila simulans. PMID:18515263
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042
Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis. PMID:18307801
Text-mining assisted regulatory annotation. PMID:18271954
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PMID:18271625
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. PMID:18226245
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. PMID:18039705
ORegAnno: an open-access community-driven resource for regulatory annotation. PMID:18006570
MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules. PMID:17997594
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
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. PMID:17550599
cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers. PMID:17490485
Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PMID:17456005
A core transcriptional network for early mesoderm development in Drosophila melanogaster. PMID:17322403
Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura. PMID:16872532 -
REDfly: the transcriptional regulatory element database for Drosophila
PubMed citations: 20.
20 articles citing: REDfly: the transcriptional regulatory element database for Drosophila
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. PMID:35886794
Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturation. PMID:35650521
Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories. PMID:35176234
Retrogene survival is not impacted by linkage relationships. PMID:35127291
regCNN: identifying Drosophila genome-wide cis-regulatory modules via integrating the local patterns in epigenetic marks and transcription factor binding motifs. PMID:35035784
Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective. PMID:34276769
Annotating the Insect Regulatory Genome. PMID:34209769
The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression. PMID:33987532
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development. PMID:33795867
Chromatin Structure and Function in Mosquitoes. PMID:33365050
The Cyclically Seasonal Drosophila subobscura Inversion O7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. PMID:33193649
Intrinsic control of muscle attachment sites matching. PMID:32706334
Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins. PMID:32681087
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. PMID:32637041
Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics. PMID:32431014
Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network. PMID:32347792
Condensin I subunit Cap-G is essential for proper gene expression during the maturation of post-mitotic neurons. PMID:32255428
Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects. PMID:31965990
Computational enhancer prediction: evaluation and improvements. PMID:30953451
Visualizing DNA folding and RNA in embryos at single-cell resolution. PMID:30886393
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More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene regulatory element
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
literature curation
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
regulation of gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
regulatory region
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
sequence feature
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
sequence motif
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 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
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
invertebrate genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
experimental design and studies
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
zoology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene regulatory element
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
literature curation
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
regulation of gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
regulatory region
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
sequence feature
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
sequence motif
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: REDfly; Regulatory Element Database for Drosophila; DOI: https://doi.org/10.25504/FAIRsharing.Q86Asf; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 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
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
invertebrate genome databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
experimental design and studies
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
zoology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
mapping
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
binding site biological regulation dna sequences gene regulatory element literature curation regulation of gene expression regulatory region sequence feature sequence motif transcription nucleic acid sequence transcription genomics invertebrate genome transcription factors and regulatory sites gene expression experimental design and studies zoology mapping
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