Drosophila DNase I footprint database
Other names: drosophila_dnase_i_footprint_database
Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.
Description
More detailed information about this field from each metasource.
Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:45.497298
Webpage:
http://www.flyreg.org/Webpage
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
PMID: 15572468
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.497298
Publications
More detailed information about this field from each metasource.
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
PMID: 15572468
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.497298
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Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
PubMed citations: 100.
100 articles citing: Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain. PMID:34982772
Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm. PMID:34687735
Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins. PMID:32681087
Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity. PMID:31223115
Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster. PMID:30739944
Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic. PMID:30383747
REDfly: the transcriptional regulatory element database for Drosophila. PMID:30329093
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
Characterization of dFOXO binding sites upstream of the Insulin Receptor P2 promoter across the Drosophila phylogeny. PMID:29200426
Identification of cis-regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response. PMID:29028826
Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development. PMID:28007888
The caste- and sex-specific DNA methylome of the termite Zootermopsis nevadensis. PMID:27848993
Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks. PMID:27600224
CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design. PMID:27487245
Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo. PMID:27152947
Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila. PMID:26975664
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. PMID:26578589
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. PMID:25779349
Incorporating chromatin accessibility data into sequence-to-expression modeling. PMID:25762337
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. PMID:25442502
Dynamic epigenetic control of highly conserved noncoding elements. PMID:25289637
Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. PMID:25173756
The Groucho co-repressor is primarily recruited to local target sites in active chromatin to attenuate transcription. PMID:25165826
Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer. PMID:24514265
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. PMID:24366875
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. PMID:24271386
Under-dominance constrains the evolution of negative autoregulation in diploids. PMID:23555226
Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. PMID:23471540
Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures. PMID:23326246
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. PMID:22893002
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. PMID:22836136
The cis-regulatory code of Hox function in Drosophila. PMID:22781127
Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites. PMID:22684627
Novel miRNAs in the control of arsenite levels in rice. PMID:22585409
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
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. PMID:21821659
Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. PMID:21310711
Genome-wide profiling of forum domains in Drosophila melanogaster. PMID:21247882
Predicting DNA-binding specificities of eukaryotic transcription factors. PMID:21152420
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
Scaffolding a Caenorhabditis nematode genome with RNA-seq. PMID:20980554
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. PMID:20965965
The gap gene network. PMID:20927566
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PMID:20862354
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
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
Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PMID:20107516
Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites. PMID:19995462
A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. PMID:19956545
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. PMID:19941641
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. PMID:19906716
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. PMID:19758432
The complex spatio-temporal regulation of the Drosophila myoblast attractant gene duf/kirre. PMID:19742310
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. PMID:19715598
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. PMID:19656951
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution. PMID:19293946
Evolution of regulatory sequences in 12 Drosophila species. PMID:19132088
Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva. PMID:19055776
Quality of regulatory elements in Drosophila retrogenes. PMID:18848618
PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling. PMID:18769735
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. PMID:18585360
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
CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. PMID:18535663
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
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
Reliable prediction of regulator targets using 12 Drosophila genomes. PMID:17989251
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
Functional conservation of Rel binding sites in drosophilid genomes. PMID:17785540
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
Improved benchmarks for computational motif discovery. PMID:17559676
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. PMID:17550599
STAMP: a web tool for exploring DNA-binding motif similarities. PMID:17478497
Integrative content-driven concepts for bioinformatics "beyond the cell". PMID:17426389
A core transcriptional network for early mesoderm development in Drosophila melanogaster. PMID:17322403
Large-scale discovery of promoter motifs in Drosophila melanogaster. PMID:17238282
SwissRegulon: a database of genome-wide annotations of regulatory sites. PMID:17130146
Large-scale turnover of functional transcription factor binding sites in Drosophila. PMID:17040121
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. PMID:16904011
Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura. PMID:16872532
Stubb: a program for discovery and analysis of cis-regulatory modules. PMID:16845069
Parametric alignment of Drosophila genomes. PMID:16789815
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. PMID:16381825
Mapping Dmef2-binding regulatory modules by using a ChIP-enriched in silico targets approach. PMID:16339902
Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. PMID:16086849
Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. PMID:15899965
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. PMID:15760844
Tags:
Tags
More detailed information about this field from each metasource.
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.497298
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.497298
dna binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.497298
nucleic acid sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:45.497298
Tags
More detailed information about this field from each metasource.
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:45.497298
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:45.497298
dna binding sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:45.497298
nucleic acid sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:45.497298
transcription factors and regulatory sites gene expression dna binding sites nucleic acid sites, features and motifs
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