CollecTF
CollecTF is a database of transcription factor binding sites (TFBS) in the Bacteria domain. It aims at becoming a reference, highly-accessed database by relying on its ability to customize navigation and data extraction, its relevance to the community, the quality and detail of the stored data and the up-to-date nature of the stored information.
Description
More detailed information about this field from each metasource.
CollecTF is a database of transcription factor binding sites (TFBS) in the Bacteria domain. It aims at becoming a reference, highly-accessed database by relying on its ability to customize navigation and data extraction, its relevance to the community, the quality and detail of the stored data and the up-to-date nature of the stored information.
metasource: Fairsharing.orgversion: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Experimentally-verified bacterial transcription factor binding sites
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://collectf.umbc.eduWebpage
More detailed information about this field from each metasource.
http://collectf.umbc.edu
metasource: Fairsharing.orgversion: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 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
Publications:
Publications
More detailed information about this field from each metasource.
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria
PMID: 24234444
metasource: Fairsharing.org
version: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkt1123
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria
PMID: 24234444
metasource: Fairsharing.org
version: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkt1123
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria
PubMed citations: 47.
47 articles citing: CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria
Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization. PMID:35216300
PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning. PMID:35135629
ECO: the Evidence and Conclusion Ontology, an update for 2022. PMID:34986598
Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714. PMID:34672328
ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts. PMID:34327299
Regulatory involvement of the PerR and SloR metalloregulators in the Streptococcus mutans oxidative stress response. PMID:33753467
Bagasse minority pathway expression: Real time study of GH2 β-mannosidases from bacteroidetes. PMID:33730062
Strain heterogeneity, cooccurrence network, taxonomic composition and functional profile of the healthy ocular surface microbiome. PMID:33622400
High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes. PMID:33579201
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. PMID:33526884
Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria. PMID:33413101
Flexible comparative genomics of prokaryotic transcriptional regulatory networks. PMID:33327941
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response. PMID:32616573
Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization. PMID:32542109
Transcription Factor Engineering for High-Throughput Strain Evolution and Organic Acid Bioproduction: A Review. PMID:32140463
A Novel Genus of Actinobacterial Tectiviridae. PMID:31817897
New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies. PMID:31712730
The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator. PMID:31681235
BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus. PMID:31500560
Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation. PMID:31429699
Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa. PMID:30980662
The Role of the CopA Copper Efflux System in Acinetobacter baumannii Virulence. PMID:30699983
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. PMID:30053267
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. PMID:29728462
ADAGE signature analysis: differential expression analysis with data-defined gene sets. PMID:29166858
Differential RNA Sequencing Implicates Sulfide as the Master Regulator of S0 Metabolism in Chlorobaculum tepidum and Other Green Sulfur Bacteria. PMID:29150516
PRODORIC2: the bacterial gene regulation database in 2018. PMID:29136200
Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans. PMID:28154810
Modelling microbial metabolic rewiring during growth in a complex medium. PMID:27881075
The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. PMID:27812948
Parametric bootstrapping for biological sequence motifs. PMID:27716039
bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. PMID:27694198
G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch. PMID:27596596
Assessment of transfer methods for comparative genomics of regulatory networks in bacteria. PMID:27586594
The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. PMID:27489856
A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. PMID:27398089
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis. PMID:27384774
SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals. PMID:27257541
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. PMID:27114493
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. PMID:26578582
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. PMID:26527724
Databases for Microbiologists. PMID:26013493
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. PMID:26013488
An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria. PMID:25986903
DMINDA: an integrated web server for DNA motif identification and analyses. PMID:24753419
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. PMID:24316579 - http://dx.doi.org/10.1093/nar/gkt1123
Tags:
Tags
More detailed information about this field from each metasource.
binding motif
metasource: Fairsharing.org
version: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
binding site
metasource: Fairsharing.org
version: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
experimentally determined
metasource: Fairsharing.org
version: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
regulation of gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 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
Tags
More detailed information about this field from each metasource.
binding motif
metasource: Fairsharing.orgversion: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
binding site
metasource: Fairsharing.orgversion: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
experimentally determined
metasource: Fairsharing.orgversion: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
regulation of gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: CollecTF; CollecTF; DOI: https://doi.org/10.25504/FAIRsharing.g2cf4x; Last edited: Dec. 19, 2019, 3:58 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
binding motif binding site experimentally determined regulation of gene expression transcription nucleic acid sequence transcription
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