RegulonDB
Names
More detailed information about this field from each metasource.
RegulonDB
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
regulondb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
Names
More detailed information about this field from each metasource.
RegulonDB
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
regulondb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
Names
More detailed information about this field from each metasource.
RegulonDB
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
regulondb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In this regard, RegulonDB is a computational model of mechanisms of transcriptional regulation.
Description
More detailed information about this field from each metasource.
RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In this regard, RegulonDB is a computational model of mechanisms of transcriptional regulation.
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
It is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. It has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
Webpage:
http://regulondb.ccg.unam.mx/Webpage
More detailed information about this field from each metasource.
http://regulondb.ccg.unam.mx/
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
Licence:
Name: RegulonDB End User Agreement and LicenceLicence name
More detailed information about this field from each metasource.
RegulonDB End User Agreement and Licence
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
More detailed information about this field from each metasource.
http://regulondb.ccg.unam.mx/menu/download/full_version/terms_and_conditions.jsp
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
PMID: 23203884
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
PMID: 26527724
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
PMID: 21051347
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
Publications
More detailed information about this field from each metasource.
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
PMID: 23203884
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
PMID: 26527724
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
PMID: 21051347
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
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RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
PubMed citations: 229.
229 articles citing: RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. PMID:35449049
Construction of Aerobic/Anaerobic-Substrate-Induced Gene Expression Procedure for Exploration of Metagenomes From Subseafloor Sediments. PMID:35095779
Predicting bacterial promoter function and evolution from random sequences. PMID:35080492
A New Sugar for an Old Phage: a c-di-GMP-Dependent Polysaccharide Pathway Sensitizes Escherichia coli for Bacteriophage Infection. PMID:34903045
Regulation of ytfK by cAMP-CRP Contributes to SpoT-Dependent Accumulation of (p)ppGpp in Response to Carbon Starvation YtfK Responds to Glucose Exhaustion. PMID:34803996
From Molecular Recognition to the "Vehicles" of Evolutionary Complexity: An Informational Approach. PMID:34769394
Quantifying the regulatory role of individual transcription factors in Escherichia coli. PMID:34758318
Decentralizing Cell-Free RNA Sensing With the Use of Low-Cost Cell Extracts. PMID:34497801
A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data. PMID:34252959
Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12. PMID:34220787
Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors. PMID:34206477
The LASER database: Formalizing design rules for metabolic engineering. PMID:34150506
Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems. PMID:33436562
Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility. PMID:32975502
Correlated chromosomal periodicities according to the growth rate and gene expression. PMID:32968121
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
OutPredict: multiple datasets can improve prediction of expression and inference of causality. PMID:32321967
Chromosomal origin of replication coordinates logically distinct types of bacterial genetic regulation. PMID:32066730
Chromatinization of Escherichia coli with archaeal histones. PMID:31692448
Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors. PMID:31445891
The Symmetrical Wave Pattern of Base-Pair Substitution Rates across the Escherichia coli Chromosome Has Multiple Causes. PMID:31266871
Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network. PMID:31116749
The E. coli transcriptional regulatory network and its spatial embedding. PMID:30879159
Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions. PMID:30842463
The Evolution of SlyA/RovA Transcription Factors from Repressors to Countersilencers in Enterobacteriaceae. PMID:30837332
Measuring cis-regulatory energetics in living cells using allelic manifolds. PMID:30570483
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. PMID:30395280
Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in Escherichia coli. PMID:30294319
Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis. PMID:30286091
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. PMID:30169674
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. PMID:30137210
Contributions of SpoT Hydrolase, SpoT Synthetase, and RelA Synthetase to Carbon Source Diauxic Growth Transitions in Escherichia coli. PMID:30123210
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. PMID:30115066
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. PMID:29745848
Regulation of Global Transcription in Escherichia coli by Rsd and 6S RNA. PMID:29686109
Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. PMID:29551268
A comprehensive evaluation of module detection methods for gene expression data. PMID:29545622
Single-target regulators form a minor group of transcription factors in Escherichia coli K-12. PMID:29529243
Transcriptional Activator GmrA, Encoded in Genomic Island OI-29, Controls the Motility of Enterohemorrhagic Escherichia coli O157:H7. PMID:29520261
Quantifying complexity in metabolic engineering using the LASER database. PMID:29468127
dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data. PMID:29467401
A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting. PMID:29433444
Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. PMID:29394395
PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli. PMID:29343727
Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure. PMID:29338696
Construction and analysis of gene-gene dynamics influence networks based on a Boolean model. PMID:29322926
Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli. PMID:29222445
Energetic funnel facilitates facilitated diffusion. PMID:29216364
Regulatory network structure determines patterns of intermolecular epistasis. PMID:29130883
Deconstructing a multiple antibiotic resistance regulation through the quantification of its input function. PMID:29018569
The interdependent network of gene regulation and metabolism is robust where it needs to be. PMID:28912490
RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study. PMID:28878825
Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli. PMID:28696257
Self-consistent theory of transcriptional control in complex regulatory architectures. PMID:28686609
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. PMID:28676075
The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase. PMID:28666008
Universal attenuators and their interactions with feedback loops in gene regulatory networks. PMID:28575450
Validating regulatory predictions from diverse bacteria with mutant fitness data. PMID:28542589
On the mechanistic nature of epistasis in a canonical cis-regulatory element. PMID:28518057
Transcriptional response of Escherichia coli to ammonia and glucose fluctuations. PMID:28447391
Strategies towards digital and semi-automated curation in RegulonDB. PMID:28365731
Enhanced construction of gene regulatory networks using hub gene information. PMID:28335719
Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. PMID:28317029
Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. PMID:28300180
LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks. PMID:28265516
Transcriptome-Level Signatures in Gene Expression and Gene Expression Variability during Bacterial Adaptive Evolution. PMID:28217741
Integrative FourD omics approach profiles the target network of the carbon storage regulatory system. PMID:28126921
Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. PMID:28115545
Genomewide landscape of gene-metabolome associations in Escherichia coli. PMID:28093455
Effects of Kasugamycin on the Translatome of Escherichia coli. PMID:28081129
Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli. PMID:28049137
What Is the Link between Stringent Response, Endoribonuclease Encoding Type II Toxin-Antitoxin Systems and Persistence? PMID:27933045
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. PMID:27933038
σ38-dependent promoter-proximal pausing by bacterial RNA polymerase. PMID:27928053
Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA. PMID:27924870
Genome-wide Escherichia coli stress response and improved tolerance towards industrially relevant chemicals. PMID:27737709
Graphlet Based Metrics for the Comparison of Gene Regulatory Networks. PMID:27695050
bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. PMID:27694198
sRNA-Mediated Control of Transcription Termination in E. coli. PMID:27662085
Bacterial persistence is an active σS stress response to metabolic flux limitation. PMID:27655400
Identification of key player genes in gene regulatory networks. PMID:27599550
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
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
The target spectrum of SdsR small RNA in Salmonella. PMID:27407104
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms. PMID:27349222
RNAlien - Unsupervised RNA family model construction. PMID:27330139
Uropathogenic Escherichia coli Metabolite-Dependent Quiescence and Persistence May Explain Antibiotic Tolerance during Urinary Tract Infection. PMID:27303698
Analysis tools for the interplay between genome layout and regulation. PMID:27294345
SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals. PMID:27257541
Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria. PMID:27242034
Control of fluxes in metabolic networks. PMID:27197218
Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation. PMID:27195891
Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. PMID:27135538
SensiPath: computer-aided design of sensing-enabling metabolic pathways. PMID:27106061
A Minimalistic Resource Allocation Model to Explain Ubiquitous Increase in Protein Expression with Growth Rate. PMID:27073913
SM-TF: A structural database of small molecule-transcription factor complexes. PMID:27010673
Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB. PMID:26980514
Intrinsic phenotypic stability of a bi-stable auto regulatory gene. PMID:26961811
Using synthetic biology to make cells tomorrow's test tubes. PMID:26952708
A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome. PMID:26951544
Selection Shapes Transcriptional Logic and Regulatory Specialization in Genetic Networks. PMID:26927540
Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. PMID:26843427
An analysis of the validity and utility of the proximon proposition. PMID:26839085
Knowledge-based three-body potential for transcription factor binding site prediction. PMID:26816396
Identification of EnvC and Its Cognate Amidases as Novel Determinants of Intrinsic Resistance to Cationic Antimicrobial Peptides. PMID:26810659
Network-Based Analysis of eQTL Data to Prioritize Driver Mutations. PMID:26802430
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. PMID:26791995
Deciphering transcriptional regulations coordinating the response to environmental changes. PMID:26772805
Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes. PMID:26766575
A Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence. PMID:26727373
Maximal Neighbor Similarity Reveals Real Communities in Networks. PMID:26680448
Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli. PMID:26653712
The quantitative and condition-dependent Escherichia coli proteome. PMID:26641532
Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli. PMID:26592556
Epistatic Interactions in the Arabinose Cis-Regulatory Element. PMID:26589997
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. PMID:26586805
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. PMID:26578589
An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network. PMID:26577401
Semi-supervised prediction of gene regulatory networks using machine learning algorithms. PMID:26564975
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes. PMID:26543854
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. PMID:26538447
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. PMID:26527724
Reciprocal Regulation of l-Arabinose and d-Xylose Metabolism in Escherichia coli. PMID:26527647
Novel gene sets improve set-level classification of prokaryotic gene expression data. PMID:26511329
sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria. PMID:26503244
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. PMID:26481353
Bacterial transcriptome reorganization in thermal adaptive evolution. PMID:26474851
Control of MarRAB Operon in Escherichia coli via Autoactivation and Autorepression. PMID:26445450
Reconstruction of novel transcription factor regulons through inference of their binding sites. PMID:26388177
Stationary-Phase Persisters to Ofloxacin Sustain DNA Damage and Require Repair Systems Only during Recovery. PMID:26330511
Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. PMID:26258987
Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth. PMID:26204448
Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task. PMID:26202448
The power of operon rearrangements for predicting functional associations. PMID:26199682
Visualizing the activity of Escherichia coli divergent promoters and probing their dependence on superhelical density using dual-colour fluorescent reporter vector. PMID:26081797
Expression noise facilitates the evolution of gene regulation. PMID:26080931
Silencing of Essential Genes within a Highly Coordinated Operon in Escherichia coli. PMID:26070674
Convergence behaviour and Control in Non-Linear Biological Networks. PMID:26068060
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks. PMID:26062809
Databases for Microbiologists. PMID:26013493
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. PMID:26013488
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. PMID:25982966
Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon. PMID:25982672
Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy. PMID:25978038
Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo. PMID:25976475
An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data. PMID:25947005
Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data. PMID:25937810
Secondary structural entropy in RNA switch (Riboswitch) identification. PMID:25928324
RSAT 2015: Regulatory Sequence Analysis Tools. PMID:25904632
Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors. PMID:25803493
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum. PMID:25765651
Spatial features for Escherichia coli genome organization. PMID:25652224
The DNA-binding network of Mycobacterium tuberculosis. PMID:25581030
Computing the functional proteome: recent progress and future prospects for genome-scale models. PMID:25576845
Identifying gene clusters by discovering common intervals in indeterminate strings. PMID:25571793
A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea. PMID:25569531
Global coordination in adaptation to gene rewiring. PMID:25564530
Scaling of gene expression with transcription-factor fugacity. PMID:25554908
The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli. PMID:25549361
Hierarchy of non-glucose sugars in Escherichia coli. PMID:25539838
Evolutionary meandering of intermolecular interactions along the drift barrier. PMID:25535374
The host metabolite D-serine contributes to bacterial niche specificity through gene selection. PMID:25526369
Promoter architecture dictates cell-to-cell variability in gene expression. PMID:25525251
Probabilistic generation of random networks taking into account information on motifs occurrence. PMID:25493547
Quantitative bacterial transcriptomics with RNA-seq. PMID:25483350
Evolution of aromatic β-glucoside utilization by successive mutational steps in Escherichia coli. PMID:25448815
Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar. PMID:25431098
Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. PMID:25380655
Characterization of the YdeO regulon in Escherichia coli. PMID:25375160
Stability depends on positive autoregulation in Boolean gene regulatory networks. PMID:25375153
iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition. PMID:25361964
Comprehensive mapping of the Escherichia coli flagellar regulatory network. PMID:25275371
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli. PMID:25266388
Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. PMID:25222563
Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds. PMID:25200799
Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks. PMID:25182846
Fur is the master regulator of the extraintestinal pathogenic Escherichia coli response to serum. PMID:25118243
IntergenicDB: a database for intergenic sequences. PMID:25097383
Detecting communities based on network topology. PMID:25033828
Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing. PMID:25006232
Conservation of transcription start sites within genes across a bacterial genus. PMID:24987095
Comparative genomics and evolution of regulons of the LacI-family transcription factors. PMID:24966856
Elucidation of operon structures across closely related bacterial genomes. PMID:24959722
Unusual interaction of RNA polymerase with the bacteriophage Mu middle promoter Pm in the absence of its activator protein Mor. PMID:24916637
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12. PMID:24903516
Metabolic shift of Escherichia coli under salt stress in the presence of glycine betaine. PMID:24858086
Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli. PMID:24837290
Antibiotics induce redox-related physiological alterations as part of their lethality. PMID:24803433
Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. PMID:24773781
DMINDA: an integrated web server for DNA motif identification and analyses. PMID:24753419
An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. PMID:24612392
The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. PMID:24603758
Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response. PMID:24603618
Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage. PMID:24586888
Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration. PMID:24580252
Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. PMID:24565265
Statistics for approximate gene clusters. PMID:24564620
Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium. PMID:24559297
Structural properties of prokaryotic promoter regions correlate with functional features. PMID:24516674
The FurA regulon in Anabaena sp. PCC 7120: in silico prediction and experimental validation of novel target genes. PMID:24503250
Review of biological network data and its applications. PMID:24465231
Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. PMID:24461193
Widespread suppression of intragenic transcription initiation by H-NS. PMID:24449106
Inflammation fuels colicin Ib-dependent competition of Salmonella serovar Typhimurium and E. coli in enterobacterial blooms. PMID:24391500
Structural control of metabolic flux. PMID:24367246
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation. PMID:24272779
Network portal: a database for storage, analysis and visualization of biological networks. PMID:24271392
Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment. PMID:24268022
Growth rate-coordinated transcriptome reorganization in bacteria. PMID:24252326
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis. PMID:24237659
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria. PMID:24234444
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. PMID:24214998
DOOR 2.0: presenting operons and their functions through dynamic and integrated views. PMID:24214966
In silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes. PMID:24187088
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
The protein interaction network of bacteriophage lambda with its host, Escherichia coli. PMID:24049175
A novel prokaryotic promoter identified in the genome of some monopartite begomoviruses. PMID:23936138
Transcription factors in Escherichia coli prefer the holo conformation. PMID:23776535
Network2Canvas: network visualization on a canvas with enrichment analysis. PMID:23749960
Integrated stress response of Escherichia coli to methylglyoxal: transcriptional readthrough from the nemRA operon enhances protection through increased expression of glyoxalase I. PMID:23646895
Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. PMID:23612296
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. PMID:23327937
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983 -
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
PubMed citations: 201.
201 articles citing: RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
PromoterLCNN: A Light CNN-Based Promoter Prediction and Classification Model. PMID:35885909
From a large-scale genomic analysis of insertion sequences to insights into their regulatory roles in prokaryotes. PMID:35725380
A successful hybrid deep learning model aiming at promoter identification. PMID:35641900
Genome-wide promoter assembly in E. coli measured at single-base resolution. PMID:35483960
Missing Links Between Gene Function and Physiology in Genomics. PMID:35295568
Sensory Systems and Transcriptional Regulation in Escherichia coli. PMID:35237580
PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning. PMID:35135629
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PMID:35130271
Disentangling direct from indirect relationships in association networks. PMID:34992138
BML: a versatile web server for bipartite motif discovery. PMID:34974623
Three topological features of regulatory networks control life-essential and specialized subsystems. PMID:34930908
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. PMID:34791440
From Molecular Recognition to the "Vehicles" of Evolutionary Complexity: An Informational Approach. PMID:34769394
Quantifying the regulatory role of individual transcription factors in Escherichia coli. PMID:34758318
Restoring Global Gene Regulation through Experimental Evolution Uncovers a NAP (Nucleoid-Associated Protein)-Like Behavior of Crp/Cap. PMID:34700380
Competitive Coherence Generates Qualia in Bacteria and Other Living Systems. PMID:34681133
Adaptation and compensation in a bacterial gene regulatory network evolving under antibiotic selection. PMID:34591012
Computational biology approaches for mapping transcriptional regulatory networks. PMID:34522292
Systematic dissection of σ70 sequence diversity and function in bacteria. PMID:34433066
Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study. PMID:34327153
Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12. PMID:34220787
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. PMID:34214468
Dynamic landscape of protein occupancy across the Escherichia coli chromosome. PMID:34170902
Recent trends in biocatalysis. PMID:34142684
The Crohn's disease-related bacterial strain LF82 assembles biofilm-like communities to protect itself from phagolysosomal attack. PMID:34035436
Bagasse minority pathway expression: Real time study of GH2 β-mannosidases from bacteroidetes. PMID:33730062
Facile accelerated specific therapeutic (FAST) platform develops antisense therapies to counter multidrug-resistant bacteria. PMID:33712689
Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations. PMID:33650807
Insights from the reanalysis of high-throughput chemical genomics data for Escherichia coli K-12. PMID:33561236
Conserved principles of transcriptional networks controlling metabolic flexibility in archaea. PMID:33525832
Adversarial generation of gene expression data. PMID:33471074
pcPromoter-CNN: A CNN-Based Prediction and Classification of Promoters. PMID:33371507
Protein dosage of the lldPRD operon is correlated with RNase E-dependent mRNA processing. PMID:33361194
Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties. PMID:33306798
Minimum Description Length Codes Are Critical. PMID:33265844
Differential Effects of Homologous Transcriptional Regulators NicR2A, NicR2B1, and NicR2B2 and Endogenous Ectopic Strong Promoters on Nicotine Metabolism in Pseudomonas sp. Strain JY-Q. PMID:33187996
Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria. PMID:33045012
A possible universal role for mRNA secondary structure in bacterial translation revealed using a synthetic operon. PMID:32973167
Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. PMID:32955440
DrpB (YedR) Is a Nonessential Cell Division Protein in Escherichia coli. PMID:32900831
Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms. PMID:32822422
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. PMID:32711472
Unraveling the Complex Interplay of Fis and IHF Through Synthetic Promoter Engineering. PMID:32626694
Programmatic access to bacterial regulatory networks with regutools. PMID:32573705
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
Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks. PMID:32487739
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks. PMID:32471360
Conserved DNA Methyltransferases: A Window into Fundamental Mechanisms of Epigenetic Regulation in Bacteria. PMID:32417228
Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework. PMID:32363397
Flux-based hierarchical organization of Escherichia coli's metabolic network. PMID:32310959
Molecular networks in Network Medicine: Development and applications. PMID:32307915
Fibration symmetries uncover the building blocks of biological networks. PMID:32234788
Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria. PMID:32182360
Excessive Promoters as Silencers of Genes Horizontally Acquired by Escherichia coli. PMID:32175329
Suppression of antibiotic resistance evolution by single-gene deletion. PMID:32144279
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. PMID:32014034
Dynamic insights on transcription initiation and RNA processing during bacterial adaptation. PMID:31992590
General and Genomic DNA-Binding Specificity for the Thermus thermophilus HB8 Transcription Factor TTHB023. PMID:31935968
The role of the bacterial protease Prc in the uropathogenesis of extraintestinal pathogenic Escherichia coli. PMID:31900139
The protein architecture in Bacteria and Archaea identifies a set of promiscuous and ancient domains. PMID:31856202
The Escherichia coli transcriptome mostly consists of independently regulated modules. PMID:31797920
Classifying Promoters by Interpreting the Hidden Information of DNA Sequences via Deep Learning and Combination of Continuous FastText N-Grams. PMID:31750297
A novel mechanism of ribonuclease regulation: GcvB and Hfq stabilize the mRNA that encodes RNase BN/Z during exponential phase. PMID:31744883
Multi-strain Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus. PMID:31738809
Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with UTIs. PMID:31633483
Systematic identification of metabolites controlling gene expression in E. coli. PMID:31578326
Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli. PMID:31527272
DIpartite: A tool for detecting bipartite motifs by considering base interdependencies. PMID:31469855
Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors. PMID:31445891
Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation. PMID:31429699
The engineering principles of combining a transcriptional incoherent feedforward loop with negative feedback. PMID:31333758
Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria. PMID:31308523
Mutations in the Global Transcription Factor CRP/CAP: Insights from Experimental Evolution and Deep Sequencing. PMID:31303977
iProEP: A Computational Predictor for Predicting Promoter. PMID:31299595
Identification and Characterization of Preferred DNA-Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA0973. PMID:31284644
Estimation of Transcription Factor Activity in Knockdown Studies. PMID:31270369
How the avidity of polymerase binding to the -35/-10 promoter sites affects gene expression. PMID:31196959
Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate. PMID:31186337
Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in Escherichia coli. PMID:31186336
Similarity corpus on microbial transcriptional regulation. PMID:31118102
Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression. PMID:31084583
A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli. PMID:31050661
Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes. PMID:30991941
Enzyme promiscuity shapes adaptation to novel growth substrates. PMID:30962359
High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription. PMID:30904377
Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli. PMID:30843055
Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions. PMID:30842463
The Evolution of SlyA/RovA Transcription Factors from Repressors to Countersilencers in Enterobacteriaceae. PMID:30837332
In silico simulations of occurrence of transcription factor binding sites in bacterial genomes. PMID:30823869
Adaptive laboratory evolution of a genome-reduced Escherichia coli. PMID:30804335
Pleiotropic effect of common PHOX2B variants in Hirschsprung disease and neuroblastoma. PMID:30799307
A versatile platform strain for high-fidelity multiplex genome editing. PMID:30788501
Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks. PMID:30786165
Mapping DNA sequence to transcription factor binding energy in vivo. PMID:30716072
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. PMID:30698741
Prioritizing bona fide bacterial small RNAs with machine learning classifiers. PMID:30697489
Evaluation of Acquired Antibiotic Resistance in Escherichia coli Exposed to Long-Term Low-Shear Modeled Microgravity and Background Antibiotic Exposure. PMID:30647159
Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance. PMID:30638812
Predicting growth rate from gene expression. PMID:30578321
A resource of variant effect predictions of single nucleotide variants in model organisms. PMID:30573687
Transcriptional Landscape of a bla KPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10. PMID:30559731
Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA. PMID:30541135
Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation. PMID:30536863
DNA sequence encodes the position of DNA supercoils. PMID:30523779
BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes. PMID:30519231
Harnessing a previously unidentified capability of bacterial allosteric transcription factors for sensing diverse small molecules in vitro. PMID:30498782
E. coli gene regulatory networks are inconsistent with gene expression data. PMID:30462289
PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence. PMID:30425888
Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes. PMID:30420454
The EcoCyc Database. PMID:30406744
Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PMID:30403660
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. PMID:30395280
In silico model-guided identification of transcriptional regulator targets for efficient strain design. PMID:30359263
wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool. PMID:30355288
Improving network inference algorithms using resampling methods. PMID:30314469
Genome-wide analysis of fitness data and its application to improve metabolic models. PMID:30305012
Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila. PMID:30283019
Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype. PMID:30282032
Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants. PMID:30256816
Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638. PMID:30248960
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. PMID:30228271
Overcoming the Cost of Positive Autoregulation by Accelerating the Response with a Coupled Negative Feedback. PMID:30208328
Grasping frequent subgraph mining for bioinformatics applications. PMID:30202444
SMRT-Cappable-seq reveals complex operon variants in bacteria. PMID:30201986
YraP Contributes to Cell Envelope Integrity and Virulence of Salmonella enterica Serovar Typhimurium. PMID:30201701
iPro70-FMWin: identifying Sigma70 promoters using multiple windowing and minimal features. PMID:30187132
Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. PMID:30175688
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. PMID:30169674
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. PMID:30137486
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. PMID:30137210
Autoregulation of bacterial gene expression: lessons from the MazEF toxin-antitoxin system. PMID:30132188
Optimal Allocation of Bacterial Protein Resources under Nonlethal Protein Maturation Stress. PMID:30122293
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. PMID:30115066
Capping-RACE: a simple, accurate, and sensitive 5' RACE method for use in prokaryotes. PMID:30107543
Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops. PMID:30096859
Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. PMID:30054360
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. PMID:30053267
Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database. PMID:30040192
Association between DSCAM polymorphisms and non-syndromic Hirschsprung disease in Chinese population. PMID:30005639
Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli. PMID:29973927
Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria. PMID:29950558
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance. PMID:29946130
A multivariate prediction model for Rho-dependent termination of transcription. PMID:29931073
On an algorithmic definition for the components of the minimal cell. PMID:29856803
Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes. PMID:29773659
70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features. PMID:29745856
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. PMID:29728462
IncGraph: Incremental graphlet counting for topology optimisation. PMID:29698494
Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-Producing Klebsiella pneumoniae. PMID:29657865
Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors. PMID:29614096
Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate. PMID:29584733
A dataset of small molecules triggering transcriptional and translational cellular responses. PMID:29556520
Single-target regulators form a minor group of transcription factors in Escherichia coli K-12. PMID:29529243
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. PMID:29490019
Selection, periodicity and potential function for Highly Iterative Palindrome-1 (HIP1) in cyanobacterial genomes. PMID:29432573
Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks. PMID:29403467
Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli. PMID:29388765
Engineering E. coli for simultaneous glucose-xylose utilization during methyl ketone production. PMID:29374483
Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation. PMID:29370758
Molecular Prediction of the O157:H-Negative Phenotype Prevalent in Australian Shiga Toxin-Producing Escherichia coli Cases Improves Concordance of In Silico Serotyping with Phenotypic Motility. PMID:29367299
Integrated analysis of motif activity and gene expression changes of transcription factors. PMID:29233921
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes. PMID:29222512
First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes. PMID:29220462
Mathematical modelling of microbes: metabolism, gene expression and growth. PMID:29187637
Conformational dynamism for DNA interaction in the Salmonella RcsB response regulator. PMID:29186528
Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci. PMID:29178959
Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation. PMID:29161365
Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics. PMID:29150605
PRODORIC2: the bacterial gene regulation database in 2018. PMID:29136200
The Transcriptional Network Structure of a Myeloid Cell: A Computational Approach. PMID:29119102
Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria. PMID:29069429
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in Escherichia coli. PMID:29046437
Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures. PMID:28981567
A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea. PMID:28973467
Efficient inference for sparse latent variable models of transcriptional regulation. PMID:28961802
Lighting up yeast cell factories by transcription factor-based biosensors. PMID:28961766
Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations. PMID:28961727
Large-scale replication study identified multiple independent SNPs in RET synergistically associated with Hirschsprung disease in Southern Chinese population. PMID:28930629
Identification and characterization of preferred DNA-binding sites for the Thermus thermophilus transcriptional regulator FadR. PMID:28902898
Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. PMID:28874552
Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli. PMID:28824593
CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. PMID:28731857
The quantitative impact of read mapping to non-native reference genomes in comparative RNA-Seq studies. PMID:28700635
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. PMID:28676075
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome. PMID:28645155
Optimizing complex phenotypes through model-guided multiplex genome engineering. PMID:28545477
ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data. PMID:28542466
Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data. PMID:28479747
Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity. PMID:28430951
Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks. PMID:28158264
Multi-resolution community detection in massive networks. PMID:27958395
A ribosome profiling study of mRNA cleavage by the endonuclease RelE. PMID:27924019
Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli. PMID:27796341
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. PMID:27713404
A Comparison of the Costs and Benefits of Bacterial Gene Expression. PMID:27711251
Overview of the interactive task in BioCreative V. PMID:27589961
Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PMID:27428627
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. PMID:27114493
Bacterial antisense RNAs are mainly the product of transcriptional noise. PMID:26973873
Indispensability of Horizontally Transferred Genes and Its Impact on Bacterial Genome Streamlining. PMID:26769030 -
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
PubMed citations: 177.
177 articles citing: RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data. PMID:35832622
Independent Component Analysis Identifies the Modulons Expanding the Transcriptional Regulatory Networks of Enterohemorrhagic Escherichia coli. PMID:35814713
Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. PMID:35449049
Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production. PMID:34989926
Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study. PMID:34327153
FINET: Fast Inferring NETwork. PMID:33172489
Globally learning gene regulatory networks based on hidden atomic regulators from transcriptomic big data. PMID:33054712
Intrinsic limitations in mainstream methods of identifying network motifs in biology. PMID:32349657
Small RNA ArcZ Regulates Oxidative Stress Response Genes and Regulons in Erwinia amylovora. PMID:31849909
Homolog comparisons further reconcile in vitro and in vivo correlations of protein activities by revealing over-looked physiological factors. PMID:31351028
Modelling and measuring intracellular competition for finite resources during gene expression. PMID:31113334
From biophysics to 'omics and systems biology. PMID:30972433
Multi-study inference of regulatory networks for more accurate models of gene regulation. PMID:30677040
Gene Expression Is Not Random: Scaling, Long-Range Cross-Dependence, and Fractal Characteristics of Gene Regulatory Networks. PMID:30459629
Detection of network motifs using three-way ANOVA. PMID:30080876
Colonization efficiency of Pseudomonas putida is influenced by Fis-controlled transcription of nuoA-N operon. PMID:30071101
Functional Prediction of Hypothetical Transcription Factors of Escherichia coli K-12 Based on Expression Data. PMID:30050664
Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database. PMID:30040192
Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data. PMID:29914350
Minimum energy control for complex networks. PMID:29453421
RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes. PMID:29361062
Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PMID:29253903
Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites. PMID:29213263
Improving GRN re-construction by mining hidden regulatory signals. PMID:29125126
The promoter region of lapA and its transcriptional regulation by Fis in Pseudomonas putida. PMID:28945818
MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections. PMID:28911113
The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner. PMID:28800583
Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data. PMID:28598965
Strategies towards digital and semi-automated curation in RegulonDB. PMID:28365731
A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain. PMID:28168783
Gene regulatory network inference using PLS-based methods. PMID:28031031
Tailor-made transcriptional biosensors for optimizing microbial cell factories. PMID:27837353
The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation. PMID:27748404
5'-Terminal AUGs in Escherichia coli mRNAs with Shine-Dalgarno Sequences: Identification and Analysis of Their Roles in Non-Canonical Translation Initiation. PMID:27467758
NrdR Transcription Regulation: Global Proteome Analysis and Its Role in Escherichia coli Viability and Virulence. PMID:27275780
SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals. PMID:27257541
Statistical analysis of structural determinants for protein-DNA-binding specificity. PMID:27147539
Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27. PMID:27137500
Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB. PMID:26980514
Gene regulatory network inference using fused LASSO on multiple data sets. PMID:26864687
H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes. PMID:26789284
Deciphering transcriptional regulations coordinating the response to environmental changes. PMID:26772805
A quantitative understanding of lac repressor's binding specificity and flexibility. PMID:26752632
The propagation of perturbations in rewired bacterial gene networks. PMID:26670742
Reconstruction of gene networks using prior knowledge. PMID:26589494
Mechanisms of mutational robustness in transcriptional regulation. PMID:26579194
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. PMID:26527724
Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli. PMID:26406465
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
Retroactivity in the Context of Modularly Structured Biomolecular Systems. PMID:26137457
CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks. PMID:26062809
Data-driven integration of genome-scale regulatory and metabolic network models. PMID:25999934
Inferring Broad Regulatory Biology from Time Course Data: Have We Reached an Upper Bound under Constraints Typical of In Vivo Studies? PMID:25984725
cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. PMID:25873626
Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors. PMID:25803493
An integrated approach to reconstructing genome-scale transcriptional regulatory networks. PMID:25723545
Pseudomonas putida Fis binds to the lapF promoter in vitro and represses the expression of LapF. PMID:25545773
Prediction of antibiotic resistance by gene expression profiles. PMID:25517437
The loose evolutionary relationships between transcription factors and other gene products across prokaryotes. PMID:25515977
Developments in the tools and methodologies of synthetic biology. PMID:25505788
OntoGene web services for biomedical text mining. PMID:25472638
Dynamic interactive events in gene regulation using E. coli dehydrogenase as a model. PMID:25433707
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. PMID:25428367
Ensemble-based network aggregation improves the accuracy of gene network reconstruction. PMID:25390635
Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression. PMID:25349675
Transfer of noncoding DNA drives regulatory rewiring in bacteria. PMID:25313052
MetaProx: the database of metagenomic proximons. PMID:25288655
Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics. PMID:25114216
A system-level model for the microbial regulatory genome. PMID:25028489
Minimal metabolic pathway structure is consistent with associated biomolecular interactions. PMID:24987116
Stochastic EM-based TFBS motif discovery with MITSU. PMID:24931999
Determining the control circuitry of redox metabolism at the genome-scale. PMID:24699140
The metabolic potential of Escherichia coli BL21 in defined and rich medium. PMID:24656150
The transcription factor titration effect dictates level of gene expression. PMID:24612990
SPIC: a novel similarity metric for comparing transcription factor binding site motifs based on information contents. PMID:24564945
Structural properties of prokaryotic promoter regions correlate with functional features. PMID:24516674
Physical constraints determine the logic of bacterial promoter architectures. PMID:24476912
Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia. PMID:24467879
Promoter-mediated transcriptional dynamics. PMID:24461023
Constraint-based models predict metabolic and associated cellular functions. PMID:24430943
Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data. PMID:24400020
Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. PMID:24296575
Analysis of fluorescent reporters indicates heterogeneity in glucose uptake and utilization in clonal bacterial populations. PMID:24238347
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis. PMID:24237659
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network. PMID:24228871
ENNET: inferring large gene regulatory networks from expression data using gradient boosting. PMID:24148309
dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data. PMID:24146601
Coupling between noise and plasticity in E. coli. PMID:24122054
Quantitative influence of macromolecular crowding on gene regulation kinetics. PMID:24121687
Bacteriophage lambda repressor mediates the formation of a complex enhancer-like structure. PMID:23989664
Comparative genomics boosts target prediction for bacterial small RNAs. PMID:23980183
A comparative analysis of industrial Escherichia coli K-12 and B strains in high-glucose batch cultivations on process-, transcriptome- and proteome level. PMID:23950949
The evolution of complex gene regulation by low-specificity binding sites. PMID:23945682
Metagenomic guilt by association: an operonic perspective. PMID:23940763
Mutation rules and the evolution of sparseness and modularity in biological systems. PMID:23936433
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. PMID:23899370
A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. PMID:23873954
Network deconvolution as a general method to distinguish direct dependencies in networks. PMID:23851448
MCOIN: a novel heuristic for determining transcription factor binding site motif width. PMID:23806098
Transcription factors in Escherichia coli prefer the holo conformation. PMID:23776535
Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. PMID:23744946
Characterization of 582 natural and synthetic terminators and quantification of their design constraints. PMID:23727987
Promoters of Escherichia coli versus promoter islands: function and structure comparison. PMID:23717391
Computational analysis of bacterial RNA-Seq data. PMID:23716638
Transcription factor binding kinetics constrain noise suppression via negative feedback. PMID:23673649
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli. PMID:23620297
A flood-based information flow analysis and network minimization method for gene regulatory networks. PMID:23617932
Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology. PMID:23610404
Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions. PMID:23599001
Indirect and suboptimal control of gene expression is widespread in bacteria. PMID:23591776
MGcV: the microbial genomic context viewer for comparative genome analysis. PMID:23547764
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. PMID:23525069
Evidence for context-dependent complementarity of non-Shine-Dalgarno ribosome binding sites to Escherichia coli rRNA. PMID:23427812
Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles. PMID:23427276
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. PMID:23398941
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. PMID:23327937
Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks. PMID:23315382
Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PMID:23271961
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. PMID:23203884
BSRD: a repository for bacterial small regulatory RNA. PMID:23203879
EcoGene 3.0. PMID:23197660
On the contributions of topological features to transcriptional regulatory network robustness. PMID:23194062
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. PMID:23173819
Coral: an integrated suite of visualizations for comparing clusterings. PMID:23102108
Evolution of transcriptional regulation in closely related bacteria. PMID:23039862
HIDEN: Hierarchical decomposition of regulatory networks. PMID:23016513
Criticality is an emergent property of genetic networks that exhibit evolvability. PMID:22969419
Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription repression. PMID:22965134
TFinDit: transcription factor-DNA interaction data depository. PMID:22943312
ncDNA and drift drive binding site accumulation. PMID:22935101
Improved predictions of transcription factor binding sites using physicochemical features of DNA. PMID:22923524
Topological effects of data incompleteness of gene regulatory networks. PMID:22920968
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PMID:22912590
Why transcription factor binding sites are ten nucleotides long. PMID:22887818
Metagenomic annotation networks: construction and applications. PMID:22879885
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. PMID:22836136
A model-based method for gene dependency measurement. PMID:22829898
The co-regulation mechanism of transcription factors in the human gene regulatory network. PMID:22798495
Wisdom of crowds for robust gene network inference. PMID:22796662
Regulatory role of cAMP receptor protein over Escherichia coli fumarase genes. PMID:22752906
PePPER: a webserver for prediction of prokaryote promoter elements and regulons. PMID:22747501
The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces. PMID:22735706
Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. PMID:22694848
Fitness landscape transformation through a single amino acid change in the rho terminator. PMID:22693458
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PMID:22693442
Regulatory component analysis: a semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge. PMID:22685363
The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective. PMID:22618875
Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria. PMID:22522891
Most networks in Wagner's model are cycling. PMID:22511935
Directed evolution as a powerful synthetic biology tool. PMID:22465795
Interpreting patterns of gene expression: signatures of coregulation, the data processing inequality, and triplet motifs. PMID:22393375
Robust detection of hierarchical communities from Escherichia coli gene expression data. PMID:22383870
Transcriptional regulation of the assT-dsbL-dsbI gene cluster in Salmonella enterica serovar Typhi IMSS-1 depends on LeuO, H-NS, and specific growth conditions. PMID:22343301
Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida. PMID:22272603
Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes. PMID:22223756
Metabolism: Amino acid regulatory wisdom. PMID:22173355
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. PMID:22156162
Conservation of Dcm-mediated cytosine DNA methylation in Escherichia coli. PMID:22150247
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PMID:22144874
Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation. PMID:22139505
The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim. PMID:22122981
Deciphering the transcriptional regulatory logic of amino acid metabolism. PMID:22082910
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. PMID:22080556
EcoliWiki: a wiki-based community resource for Escherichia coli. PMID:22064863
Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella. PMID:22035052
Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation. PMID:21961582
Recognition of prokaryotic promoters based on a novel variable-window Z-curve method. PMID:21954440
Membrane stresses induced by overproduction of free fatty acids in Escherichia coli. PMID:21948837
Redefining Escherichia coli σ(70) promoter elements: -15 motif as a complement of the -10 motif. PMID:21908667
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. PMID:21864382
Bile salts induce resistance to polymyxin in enterohemorrhagic Escherichia coli O157:H7. PMID:21725004
RSAT 2011: regulatory sequence analysis tools. PMID:21715389
Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities. PMID:21668997
A computational framework for gene regulatory network inference that combines multiple methods and datasets. PMID:21489290
Bacterial transcription terminators: the RNA 3'-end chronicles. PMID:21439297
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:21177655
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biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
regulation of gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
molecular interactions, pathways and networks
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
gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.086297
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
regulation of gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: RegulonDB; RegulonDB; DOI: https://doi.org/10.25504/FAIRsharing.f0awr5; Last edited: April 26, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
gene transcripts
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:48.086297
biological regulation dna regulation of gene expression rna transcription transcription factors and regulatory sites molecular interactions, pathways and networks gene expression gene transcripts
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