RegPrecise

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RegPrecise

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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regprecise

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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Other names: regprecise

Predicted regulons in prokaryotic genomes

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Publications

More detailed information about this field from each metasource. ×

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
PMID: 19884135

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics
PMID: 22700702

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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http://nar.oxfordjournals.org/content/38/suppl_1/D111

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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• RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes PubMed citations: 110.

  110 articles citing: RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

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  Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing. PMID:33853520

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  Streptococcus pneumoniae metal homeostasis alters cellular metabolism. PMID:32676626

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  Pyruvate secretion by oral streptococci modulates hydrogen peroxide dependent antagonism. PMID:31988475

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  Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium. PMID:31585844

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  EtcABC, a Putative EII Complex, Regulates Type 3 Fimbriae via CRP-cAMP Signaling in Klebsiella pneumoniae. PMID:31354661

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  Greedy de novo motif discovery to construct motif repositories for bacterial proteomes. PMID:30999854

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  Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria. PMID:30249705

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  NADH-Mediated Gene Expression in Streptococcus pneumoniae and Role of Rex as a Transcriptional Repressor of the Rex-Regulon. PMID:29971050

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  Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization. PMID:29740413

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  Niacin-mediated Gene Expression and Role of NiaR as a Transcriptional Repressor of niaX, nadC, and pnuC in Streptococcus pneumoniae. PMID:28337428

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  A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain. PMID:28168783

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  Cysteine-Mediated Gene Expression and Characterization of the CmbR Regulon in Streptococcus pneumoniae. PMID:27990139

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  N-acetylglucosamine-Mediated Expression of nagA and nagB in Streptococcus pneumoniae. PMID:27900287

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  Negative Regulation of Ectoine Uptake and Catabolism in Sinorhizobium meliloti: Characterization of the EhuR Gene. PMID:27795315

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  Cap0037, a Novel Global Regulator of Clostridium acetobutylicum Metabolism. PMID:27703070

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  N-acetylgalatosamine-Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae. PMID:27672623

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  An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes. PMID:27507169

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  A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. PMID:27398089

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  SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals. PMID:27257541

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  Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data. PMID:27047450

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  A quantitative understanding of lac repressor's binding specificity and flexibility. PMID:26752632

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  Global Regulator IscR Positively Contributes to Antimonite Resistance and Oxidation in Comamonas testosteroni S44. PMID:26734615

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  HexR Controls Glucose-Responsive Genes and Central Carbon Metabolism in Neisseria meningitidis. PMID:26644430

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  Functional role of pyruvate kinase from Lactobacillus bulgaricus in acid tolerance and identification of its transcription factor by bacterial one-hybrid. PMID:26581248

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  A novel transcriptional regulator of L-arabinose utilization in human gut bacteria. PMID:26438537

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  Reconstruction of novel transcription factor regulons through inference of their binding sites. PMID:26388177

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  Conserved and divergent functions of RcrRPQ in Streptococcus gordonii and S. mutans. PMID:26229070

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  The regulatory function of LexA is temperature-dependent in the deep-sea bacterium Shewanella piezotolerans WP3. PMID:26150814

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  The Crystal Structure of Thermotoga maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site. PMID:26147435

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  Maltose-Dependent Transcriptional Regulation of the mal Regulon by MalR in Streptococcus pneumoniae. PMID:26030923

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  cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. PMID:25873626

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  Sialic acid-mediated gene expression in Streptococcus pneumoniae and role of NanR as a transcriptional activator of the nan gene cluster. PMID:25724955

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  A new regulatory mechanism for bacterial lipoic acid synthesis. PMID:25611823

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  Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates. PMID:25536074

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  Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities. PMID:25294412

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  Comparison of genes required for H2O2 resistance in Streptococcus gordonii and Streptococcus sanguinis. PMID:25280752

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  Regulation of fatty acid biosynthesis by the global regulator CcpA and the local regulator FabT in Streptococcus mutans. PMID:25131436

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  Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. PMID:25002542

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  Conservation of transcription start sites within genes across a bacterial genus. PMID:24987095

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  LacR is a repressor of lacABCD and LacT is an activator of lacTFEG, constituting the lac gene cluster in Streptococcus pneumoniae. PMID:24951784

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  Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton. PMID:24884510

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  Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. PMID:24865553

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  PdhR, the pyruvate dehydrogenase repressor, does not regulate lipoic acid synthesis. PMID:24816490

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  Streptococcus pyogenes polymyxin B-resistant mutants display enhanced ExPortal integrity. PMID:24794568

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  DMINDA: an integrated web server for DNA motif identification and analyses. PMID:24753419

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  Diversity of the metal-transporting P1B-type ATPases. PMID:24729073

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  Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. PMID:24639670

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  Effect of bodily fluids from honey bee (Apis mellifera) larvae on growth and genome-wide transcriptional response of the causal agent of American Foulbrood disease (Paenibacillus larvae). PMID:24586572

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  Computational analysis of riboswitch-based regulation. PMID:24583554

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  Metal binding properties of Escherichia coli YjiA, a member of the metal homeostasis-associated COG0523 family of GTPases. PMID:24449932

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  Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network. PMID:24228871

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  Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. PMID:24196194

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  RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. PMID:24175918

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  Methionine biosynthesis in Staphylococcus aureus is tightly controlled by a hierarchical network involving an initiator tRNA-specific T-box riboswitch. PMID:24068926

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  Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. PMID:24060102

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  Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. PMID:23995632

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  Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. PMID:23986752

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  Stationary phase and nutrient levels trigger transcription of a genomic locus containing a novel peptide (TM1316) in the hyperthermophilic bacterium Thermotoga maritima. PMID:23974142

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  Aureolib - a proteome signature library: towards an understanding of staphylococcus aureus pathophysiology. PMID:23967085

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  New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. PMID:23913324

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  Hidden Markov models for evolution and comparative genomics analysis. PMID:23762278

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  Brucella BioR regulator defines a complex regulatory mechanism for bacterial biotin metabolism. PMID:23729648

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  The genome organization of Thermotoga maritima reflects its lifestyle. PMID:23637642

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  Indirect and suboptimal control of gene expression is widespread in bacteria. PMID:23591776

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  Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PMID:23555977

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  RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. PMID:23547897

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  MGcV: the microbial genomic context viewer for comparative genome analysis. PMID:23547764

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  Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. PMID:23504016

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  Cellobiose-mediated gene expression in Streptococcus pneumoniae: a repressor function of the novel GntR-type regulator BguR. PMID:23469031

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  Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. PMID:23398941

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  Inference of gene regulatory networks from genome-wide knockout fitness data. PMID:23271269

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  Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. PMID:23209028

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  Quinolinate salvage and insights for targeting NAD biosynthesis in group A streptococci. PMID:23204464

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  Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. PMID:23086211

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  The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element. PMID:23043002

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  Evolution of transcriptional regulation in closely related bacteria. PMID:23039862

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  Regulation of neuraminidase expression in Streptococcus pneumoniae. PMID:22963456

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  Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. PMID:22925190

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  Diversity and versatility of the Thermotoga maritima sugar kinome. PMID:22885293

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  PePPER: a webserver for prediction of prokaryote promoter elements and regulons. PMID:22747501

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  N-acetylgalactosamine utilization pathway and regulon in proteobacteria: genomic reconstruction and experimental characterization in Shewanella. PMID:22711537

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  RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. PMID:22700702

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  Phenylacetic acid catabolism and its transcriptional regulation in Corynebacterium glutamicum. PMID:22685150

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  Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. PMID:22638572

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  Mining genomes of marine cyanobacteria for elements of zinc homeostasis. PMID:22514551

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  The major facilitator superfamily (MFS) revisited. PMID:22458847

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  A functional genomics approach to establish the complement of carbohydrate transporters in Streptococcus pneumoniae. PMID:22428019

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  CcpA regulates biofilm formation and competence in Streptococcus gordonii. PMID:22394467

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  Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases. PMID:22247137

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  Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. PMID:22210771

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  Ribulokinase and transcriptional regulation of arabinose metabolism in Clostridium acetobutylicum. PMID:22194461

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  Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins. PMID:22192777

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  Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. PMID:22135468

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  Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PMID:22125499

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  Phylogenetic footprinting: a boost for microbial regulatory genomics. PMID:22113593

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  Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals. PMID:21953179

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  The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. PMID:21884625

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  Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis. PMID:21849503

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  Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. PMID:21840973

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  Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. PMID:21810205

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  Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria. PMID:21622752

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  Comparative genomics of the dormancy regulons in mycobacteria. PMID:21602344

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  Environmental influences on competitive hydrogen peroxide production in Streptococcus gordonii. PMID:21571883

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  Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. PMID:21531804

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  Role of a Zn-independent DksA in Zn homeostasis and stringent response. PMID:21255113

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  RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). PMID:21051347

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  Catabolite control protein A controls hydrogen peroxide production and cell death in Streptococcus sanguinis. PMID:21036992

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  Genomics-driven reconstruction of acinetobacter NAD metabolism: insights for antibacterial target selection. PMID:20926389

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  Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. PMID:20836887

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  RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. PMID:20542910
• RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics PubMed citations: 14.

  14 articles citing: RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

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  MntP and YiiP Contribute to Manganese Efflux in Salmonella enterica Serovar Typhimurium under Conditions of Manganese Overload and Nitrosative Stress. PMID:35019706

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  Calprotectin-Mediated Zinc Chelation Inhibits Pseudomonas aeruginosa Protease Activity in Cystic Fibrosis Sputum. PMID:33927050

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  Pyruvate secretion by oral streptococci modulates hydrogen peroxide dependent antagonism. PMID:31988475

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  Bacterial zinc uptake regulator proteins and their regulons. PMID:30065104

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  Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model. PMID:27567672

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  SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals. PMID:27257541

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  DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems. PMID:25079303

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  Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing. PMID:24781900

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  Computational analysis of riboswitch-based regulation. PMID:24583554

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  Network portal: a database for storage, analysis and visualization of biological networks. PMID:24271392

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  RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. PMID:24175918

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  Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. PMID:24060102

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  Aureolib - a proteome signature library: towards an understanding of staphylococcus aureus pathophysiology. PMID:23967085

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  EcoCyc: fusing model organism databases with systems biology. PMID:23143106
• http://nar.oxfordjournals.org/content/38/suppl_1/D111

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More detailed information about this field from each metasource. ×

nucleotide sequence databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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transcriptional regulator sites and transcription factors

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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transcription factors and regulatory sites

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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gene expression

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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dna binding sites

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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molecular interactions, pathways and networks

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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nucleic acid sites, features and motifs

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:19.169917

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nucleic acid sequence transcription transcription factors and regulatory sites gene expression dna binding sites molecular interactions, pathways and networks nucleic acid sites, features and motifs