Cited by 368Bacterial Genetics and BiotechnologyGene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

Open access

Salgado, H.·2006·Nucleic Acids Research

DOI 10.1093/nar/gkj156PMC PMC1347518

Open this paper in CoChat — free account Open PDF

Abstract

RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge of the regulatory network and operon organization. It is currently the largest electronically-encoded database of the regulatory network of any free-living organism. We present here the recently launched RegulonDB version 5.0 radically different in content, interface design and capabilities. Continuous curation of original scientific literature provides the evidence behind every single object and feature. This knowledge is complemented with comprehensive computational predictions across the complete genome. Literature-based and predicted data are clearly distinguished in the database. Starting with this version, RegulonDB public releases are synchronized with those of EcoCyc since our curation supports both databases. The complex biology of regulation is simplified in a navigation scheme based on three major streams: genes, operons and regulons. Regulatory knowledge is directly available in every navigation step. Displays combine graphic and textual information and are organized allowing different levels of detail and biological context. This knowledge is the backbone of an integrated system for the graphic display of the network, graphic and tabular microarray comparisons with curated and predicted objects, as well as predictions across bacterial genomes, and predicted networks of functionally related gene products. Access RegulonDB at http://regulondb.ccg.unam.mx.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/nar/gkj156

Cites

25 of 25 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Network motifs in the transcriptional regulation network of Escherichia coli
Shen-Orr, S. S., Milo, R., Mangan, S., & Alon, U. S. (2002) · Nature Genetics · doi:10.1038/ng881 · Cited by 2,970
EcoCyc: a comprehensive database resource for Escherichia coli
Keseler, I. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki108 · Cited by 737
Identifying global regulators in transcriptional regulatory networks in bacteria
Martínez‐Antonio, A., & Collado‐Vides, J. (2003) · Current Opinion in Microbiology · doi:10.1016/j.mib.2003.09.002 · Cited by 547
Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli
Cooper, T. F., Rozen, D. E., & Lenski, R. E. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334340100 · Cited by 440
Operons in Escherichia coli: genomic analyses and predictions.
Salgado, H., Moreno-Hagelsieb, G., Smith, T., & Collado-Vides, J. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.110147297 · Cited by 411
Self-citation
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
Salgado, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh140 · Cited by 262
Self-citation
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12
Salgado, H. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.72 · Cited by 256
Self-citation
Sigma70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Overlapping Promoter-like Signals
Huerta, A. M., & Collado‐Vides, J. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.07.017 · Cited by 233
Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica
Zwir, I. J. S., Shin, D., Kato, A., Nishino, K., Latifi, T. N., Solomon, F., Hare, J. M., Huang, H. V., & Groisman, E. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408238102 · Cited by 210
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
Ma, H.-W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh1009 · Cited by 208

Show all 25 references

Sorted by citations

Items 101–200 of 368

GENERALIZED HILL FUNCTION METHOD FOR MODELING MOLECULAR PROCESSES
Likhoshvai, V. A., & Ratushny, A. V. (2007) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720007002837 · Cited by 54
A comparison of key aspects of gene regulation in S treptomyces coelicolor and E scherichia coli using nucleotide‐resolution transcription maps produced in parallel by global and differential RNA sequencing
Romero, D. A., Hasan, A. H., Lin, Y., Kime, L., Ruiz‐Larrabeiti, O., Urem, M., Bucca, G., Mamanova, L., Laing, E., van Wezel, G. P., et al. (2014) · Molecular Microbiology · doi:10.1111/mmi.12810 · Cited by 52
Evaluation of Swine-Specific PCR Assays Used for Fecal Source Tracking and Analysis of Molecular Diversity of Swine-Specific “ Bacteroidales ” Populations
Lamendella, R., Domingo, J. W. S., Yannarell, A. C., Ghosh, S., Giovanni, G. D., Mackie, R. I., & Oerther, D. B. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00448-09 · Cited by 52
Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks
Ma’ayan, A., Cecchi, G., Wagner, J., Rao, A. R., Iyengar, R., & Stolovitzky, G. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805344105 · Cited by 51
Structure and evolution of gene regulatory networks in microbial genomes
Janga, S. C., & Collado‐Vides, J. (2007) · Research in Microbiology · doi:10.1016/j.resmic.2007.09.001 · Cited by 50
Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach
Freyre-González, J. A., Alonso-Pavón, J. A., Treviño-Quintanilla, L. G., & Collado‐Vides, J. (2008) · Genome biology · doi:10.1186/gb-2008-9-10-r154 · Cited by 49
Genotype and Phenotypes of an Intestine-Adapted Escherichia coli K-12 Mutant Selected by Animal Passage for Superior Colonization
Fabich, A. J., Leatham, M. P., Grissom, J. E., Wiley, G. B., Lai, H., Najar, F. Z., Roe, B. A., Cohen, P. S., & Conway, T. (2011) · Infection and Immunity · doi:10.1128/iai.01199-10 · Cited by 46
Detecting gene clusters under evolutionary constraint in a large number of genomes
Ling, X., He, X., & Xin, D. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp027 · Cited by 48
Selection for Unequal Densities of σ70 Promoter-Like Signals in Different Regions of Large Bacterial Genomes
Huerta, A. M., Francino, M. P., Morett, E., & Collado‐Vides, J. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020185 · Cited by 48
Adversarial generation of gene expression data
Viñas, R., Andrés-Terré, H., Lió, P., & Bryson, K. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab035 · Cited by 47
A multi-approaches-guided genetic algorithm with application to operon prediction
Wang, S., Wang, Y., Du, W., Sun, F., Wang, X., Zhou, C., & Liang, Y. (2007) · Artificial Intelligence in Medicine · doi:10.1016/j.artmed.2007.07.010 · Cited by 46
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
Janky, R., & van Helden, J. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-37 · Cited by 45
The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks
Lozada-Chávez, I., Angarica, V. E., Collado‐Vides, J., & Contreras‐Moreira, B. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.04.008 · Cited by 49
Analysis of gene expression in operons of Streptomyces coelicolor
Laing, E., Mersinias, V., Smith, C. P. S., & Hubbard, S. J. (2006) · Genome biology · doi:10.1186/gb-2006-7-6-r46 · Cited by 44
Ranking of network elements based on functional substructures
Koschützki, D., Schwöbbermeyer, H., & Schreiber, F. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.05.038 · Cited by 43
Proximity of intracellular regulatory networks to monotone systems
Ma’ayan, A., Lipshtat, A., Iyengar, R., & Sontag, E. D. (2008) · IET Systems Biology · doi:10.1049/iet-syb:20070036 · Cited by 43
Methods to Reconstruct and Compare Transcriptional Regulatory Networks
Babu, M. M., Lang, B., & Aravind, L. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-243-4_8 · Cited by 42
Discovering Sequence Motifs
Bailey, T. L. (2008) · Methods in molecular biology · doi:10.1007/978-1-60327-159-2_12 · Cited by 40
Structural Coupling between RNA Polymerase Composition and DNA Supercoiling in Coordinating Transcription: a Global Role for the Omega Subunit?
Geertz, M., TRAVERS, A. A., Mehandziska, S., Sobetzko, P., Janga, S. C., Shimamoto, N., & Muskhelishvili, G. (2011) · mBio · doi:10.1128/mbio.00034-11 · Cited by 40
Mechanism of phage sensing and restriction by toxin-antitoxin-chaperone systems
Mets, T., Kurata, T., Ernits, K., Johansson, M., Craig, S. Z., Evora, G. M., Buttress, J. A., Odai, R., Wallant, K. C. ’., Nakamoto, J. A., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.05.003 · Cited by 38
Literature-based priors for gene regulatory networks
Steele, E., Tucker, A., Hoen, P. A. C. ’., & Schuemie, M. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp277 · Cited by 39
Engineering regulatory networks for complex phenotypes in E. coli
Liu, R., Liang, L., Freed, E. F., Choudhury, A., Eckert, C. A., & Gill, R. T. (2020) · Nature Communications · doi:10.1038/s41467-020-17721-4 · Cited by 37
Discovering Sequence Motifs
Bailey, T. L. (2007) · Methods in molecular biology · doi:10.1007/978-1-59745-514-5_17 · Cited by 39
Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio
Lintner, R. E., Mishra, P. K., Srivastava, P., Martínez-Vaz, B. M., Khodursky, A. B., & Blumenthal, R. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-60 · Cited by 40
Operon prediction in Pyrococcus furiosus
Tran, T., Dam, P., Su, Z., Poole, F. L., Adams, M. W. W., Zhou, G. T., & Xu, Y. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl974 · Cited by 38
Co-evolution of transcription factors and their targets depends on mode of regulation
Hershberg, R., & Margalit, H. (2006) · Genome biology · doi:10.1186/gb-2006-7-7-r62 · Cited by 37
Biophysically Motivated Regulatory Network Inference: Progress and Prospects
Äijö, T., & Bonneau, R. (2016) · Human Heredity · doi:10.1159/000446614 · Cited by 30
Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet
経男, 岩., Wittkop, T., Kleindt, C. K., & Tauch, A. (2009) · Nature Protocols · doi:10.1038/nprot.2009.81 · Cited by 37
Application of Molecular Techniques To Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site
Field, E. K., D’Imperio, S., Miller, A. R., VanEngelen, M. R., Gerlach, R., Lee, B. D., Apel, W. A., & Peyton, B. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.01688-09 · Cited by 36
Reconstruction of Biological Networks by Supervised Machine Learning Approaches
Vert, J. (2010) · doi:10.1002/9780470556757.ch7 · Cited by 36
Fast computing global structural balance in signed networks based on memetic algorithm
Sun, Y., Du, H., Gong, M., Ma, L., & Wang, S. (2014) · Physica A Statistical Mechanics and its Applications · doi:10.1016/j.physa.2014.07.071 · Cited by 35
Consensus and Meta-analysis regulatory networks for combining multiple microarray gene expression datasets
Steele, E., & Tucker, A. (2008) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2008.01.011 · Cited by 35
Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators
Ishihama, A., & Shimada, T. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab032 · Cited by 34
Discerning static and causal interactions in genome-wide reverse engineering problems
Zampieri, M., Soranzo, N., & Altafini, C. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn220 · Cited by 34
Size matters: network inference tackles the genome scale
Hayete, B., Gardner, T. S., & Collins, J. J. (2007) · Molecular Systems Biology · doi:10.1038/msb4100118 · Cited by 33
Model-based redesign of global transcription regulation
Carrera, J., Rodrigo, G., & Jaramillo, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp022 · Cited by 36
Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets
Shimada, T., Saito, N., Maeda, M., Tanaka, K., & Ishihama, A. (2015) · Microbial Genomics · doi:10.1099/mgen.0.000001 · Cited by 32
Linking Cytoscape and the corynebacterial reference database CoryneRegNet
Baumbach, J., & Apeltsin, L. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-184 · Cited by 32
The magnitude and colour of noise in genetic negative feedback systems
Voliotis, M., & Bowsher, C. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks385 · Cited by 32
How Little Do We Actually Know? On the Size of Gene Regulatory Networks
Röttger, R., Rückert, U., Taubert, J., & Baumbach, J. (2012) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2012.71 · Cited by 32
A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions
Lagani, V., Karozou, A. D., Gómez-Cabrero, D., Silberberg, G., & Tsamardinos, I. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1038-1 · Cited by 32
Integrated bioinformatic and phenotypic analysis of RpoN‐dependent traits in the plant growth‐promoting bacterium Pseudomonas fluorescens SBW25
Jones, J., Studholme, D. J., Cg, K., & Preston, G. M. (2007) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01416.x · Cited by 32
CRP Binding and Transcription Activation at CRP-S Sites
Cameron, A. D. S., & Redfield, R. J. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.08.027 · Cited by 31
A global analysis of adaptive evolution of operons in cyanobacteria
Memon, D., Singh, A. K., Pakrasi, H. B., & Wangikar, P. P. (2012) · Antonie van Leeuwenhoek · doi:10.1007/s10482-012-9813-0 · Cited by 31
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease
Lin, Y., David Romero, A., Guan, S., Mamanova, L., & McDowall, K. J. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-620 · Cited by 30
Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles
Moreno‐Hagelsieb, G., & Janga, S. C. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21564 · Cited by 30
In silico network topology-based prediction of gene essentiality
da Silva, J. P. M., Acencio, M. L., Mombach, J. C. M., Vieira, R. L. R., da Silva, J. C., Lemke, N., & Sinigaglia, M. (2007) · Physica A Statistical Mechanics and its Applications · doi:10.1016/j.physa.2007.10.044 · Cited by 29
On the power and limits of evolutionary conservation—unraveling bacterial gene regulatory networks
Baumbach, J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq699 · Cited by 29
CoryneRegNet 3.0—An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli
Baumbach, J., Wittkop, T., Rademacher, K., Rahmann, S., Brinkrolf, K., & Tauch, A. (2006) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2006.12.012 · Cited by 28
A modeling and computational study of the frustration index in signed networks
Aref, S., Mason, A., & Wilson, M. C. (2019) · Networks · doi:10.1002/net.21907 · Cited by 28
Formation of the Open Complex by Bacterial RNA Polymerase—A Quantitative Model
Djordjević, M., & Bundschuh, R. A. (2008) · Biophysical Journal · doi:10.1529/biophysj.107.116970 · Cited by 28
Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli
Janga, S. C., Salgado, H., Martínez‐Antonio, A., & Collado‐Vides, J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm743 · Cited by 27
Self-citation
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes
González-Pérez, A., Angarica, V. E., de Vasconcelos, A. T. R., & Collado‐Vides, J. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl800 · Cited by 27
BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks
Guziołowski, C., Bourdé, A., Moreews, F., & Siegel, A. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-244 · Cited by 25
Cost-Aware Robust Control of Signed Networks by Using a Memetic Algorithm
Ma, L., Li, J., Lin, Q., Gong, M., Coello, C. A. C., & Ming, Z. (2019) · IEEE Transactions on Cybernetics · doi:10.1109/tcyb.2019.2932996 · Cited by 26
Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations
Zare, H., Sangurdekar, D. P., Srivastava, P., Kaveh, M., & Khodursky, A. B. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-39 · Cited by 25
Genome Holography: Deciphering Function-Form Motifs from Gene Expression Data
Madi, A., Friedman, Y., Roth, D., Regev, T. I., Bransburg‐Zabary, S., & Jacob, E. B. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002708 · Cited by 25
A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences
Bi, C. (2008) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2008.103 · Cited by 25
Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks
Iacono, G., & Altafini, C. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-83 · Cited by 25
Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences
Jahn, K. (2011) · Journal of Computational Biology · doi:10.1089/cmb.2011.0132 · Cited by 25
An evolutionary game approach for determination of the structural conflicts in signed networks
Tan, S., & Lü, J. (2016) · Scientific Reports · doi:10.1038/srep22022 · Cited by 24
Functional annotation of regulatory pathways
Pandey, J., Koyutürk, M., Kim, Y.-H., Wojciech Szpankowski, A., Subramaniam, S., & Grama, A. Y. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm203 · Cited by 24
Scaling relationship in the gene content of transcriptional machinery in bacteria
Pérez‐Rueda, E., Janga, S. C., & Martínez‐Antonio, A. (2009) · Molecular BioSystems · doi:10.1039/b907384a · Cited by 25
Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor
Laing, E., Sidhu, K., & Hubbard, S. J. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-79 · Cited by 23
Computational operon prediction in whole-genomes and metagenomes
Zaidi, S. S. A., & Zhang, X. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw034 · Cited by 23
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks
Baumbach, J., Tauch, A., & Rahmann, S. (2008) · Briefings in Bioinformatics · doi:10.1093/bib/bbn055 · Cited by 23
The Sugar Phosphotransferase System of Vibrio fischeri Inhibits both Motility and Bioluminescence
Visick, K. L., O'Shea, T. M., Klein, A. H., Geszvain, K., & Wolfe, A. J. (2007) · Journal of Bacteriology · doi:10.1128/jb.01761-06 · Cited by 23
The Role of Mutational Dynamics in Genome Shrinkage
van Hoek, M. J. A., & Hogeweg, P. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm183 · Cited by 23
Comparative footprinting of DNA-binding proteins
Contreras‐Moreira, B., & Collado‐Vides, J. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl215 · Cited by 23
Genomic Arrangement of Regulons in Bacterial Genomes
Zhang, H., Yin, Y., Olman, V. N., & Xu, Y. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029496 · Cited by 21
Bacterial glycobiotechnology: A biosynthetic route for the production of biopharmaceutical glycans
Paliya, B. S., Sharma, V. K., Tuohy, M. G., Singh, H. B., Koffas, M. A. G., Benhida, R., Tiwari, B. K., Kalaskar, D. M., Singh, B. N., & Gupta, V. K. (2023) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108180 · Cited by 21
Genome-wide partial correlation analysis of Escherichia coli microarray data.
Veiga, D. F. T., Vicente, F. F. D. R., Grivet, M., de la Fuente, A., & de Vasconcelos, A. T. R. (2007) · PubMed · Cited by 21
Evidence classification of high-throughput protocols and confidence integration in RegulonDB
Weiss, V., Medina-Rivera, A., Huerta, A. M., Santos-Zavaleta, A., Salgado, H., Morett, E., & Collado‐Vides, J. (2013) · Database · doi:10.1093/database/bas059 · Cited by 20
Self-citation
Development of a Biosensor Platform for Phenolic Compounds Using a Transition Ligand Strategy
Flachbart, L. K., Gertzen, C. G. W., Gohlke, H., & Marienhagen, J. (2021) · ACS Synthetic Biology · doi:10.1021/acssynbio.1c00165 · Cited by 20
Post‐transcriptional regulatory networks play a key role in noise reduction that is conserved from micro‐organisms to mammals
Joshi, A., Beck, Y., & Michoel, T. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08571.x · Cited by 21
BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference
Pirayre, A., Couprie, C., Bidard, F., Duval, L. C., & Pesquet, J.-C. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0754-2 · Cited by 19
Predicting protein linkages in bacteria: Which method is best depends on task
Karimpour‐Fard, A., Leach, S. M., Gill, R. T., & Hunter, L. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-397 · Cited by 19
Towards the automated engineering of a synthetic genome
Carrera, J., Rodrigo, G., & Jaramillo, A. (2009) · Molecular BioSystems · doi:10.1039/b904400k · Cited by 18
Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae
Guzmán-Vargas, L., & Santillán, M. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-13 · Cited by 18
iMTF-GRN: Integrative Matrix Tri-Factorization for Inference of Gene Regulatory Networks
Wani, N., & Raza, K. (2019) · IEEE Access · doi:10.1109/access.2019.2936794 · Cited by 18
INTRAGENIC PROMOTOR-LIKE SITES IN THE GENOME OFESCHERICHIA COLIDISCOVERY AND FUNCTIONAL IMPLICATION
Tutukina, M. N., Shavkunov, K. S., Masulis, I. S., & Ozoline, O. N. (2007) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720007002801 · Cited by 18
An Assessment of the Role of DNA Adenine Methyltransferase on Gene Expression Regulation in E coli
Seshasayee, A. S. N. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000273 · Cited by 18
General Trends in the Evolution of Prokaryotic Transcriptional Regulatory Networks
Babu, M. M., Balaji, S., & Aravind, L. (2007) · KARGER eBooks · doi:10.1159/000107604 · Cited by 18
Inferring Transcriptional Interactions and Regulator Activities from Experimental Data
Wang, R., Zhang, X.-S., & Chen, L. (2007) · Molecules and Cells · doi:10.1016/s1016-8478(23)07344-2 · Cited by 17
Extracting Regulatory Networks of Escherichia coli from RegulonDB
Salgado, H., Martínez‐Flores, I., López-Fuentes, A., García-Sotelo, J. S., Porrón-Sotelo, L., Solano-Lira, H., Muñiz-Rascado, L., & Collado‐Vides, J. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-361-5_10 · Cited by 16
Self-citation
The cis-regulatory map of Shewanella genomes
Liu, J., Xu, X., & Stormo, G. D. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn515 · Cited by 16
Internal Versus External Effector and Transcription Factor Gene Pairs Differ in Their Relative Chromosomal Position in Escherichia coli
Janga, S. C., Salgado, H., Collado‐Vides, J., & Martínez‐Antonio, A. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.01.019 · Cited by 16
Self-citation
Inferring the role of transcription factors in regulatory networks
Veber, P., Guziołowski, C., Borgne, M. L., Radulescu, O., & Siegel, A. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-228 · Cited by 16
Prediction and Integration of Regulatory and Protein–Protein Interactions
Wichadakul, D., McDermott, J., & Samudrala, R. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-243-4_6 · Cited by 15
What Determines the Assembly of Transcriptional Network Motifs in Escherichia coli?
Camas, F. M., & Poyatos, J. F. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003657 · Cited by 15
Is Thermosensing Property of RNA Thermometers Unique?
Shah, P., & Gilchrist, M. A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011308 · Cited by 16
Deterministic local alignment methods improved by a simple genetic algorithm
Bi, C. (2010) · Neurocomputing · doi:10.1016/j.neucom.2010.01.023 · Cited by 15
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies
Thiele, S., Cerone, L., Sáez-Rodríguez, J., Siegel, A., Guziołowski, C., & Klamt, S. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0733-7 · Cited by 18
Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families
Janga, S. C., & Pérez‐Rueda, E. (2009) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2009.06.004 · Cited by 15
Horizontally transferred genes cluster spatially and metabolically
Dilthey, A., & Lercher, M. J. (2015) · Biology Direct · doi:10.1186/s13062-015-0102-5 · Cited by 15
An Exact Method for Computing the Frustration Index in Signed Networks Using Binary ProgrammingPreprint
Arefkashfi, S., Mason, A., & Wilson, M. C. (2016) · arXiv (Cornell University) · Cited by 15
Computing the Line Index of Balance Using Integer Programming Optimisation
Aref, S., Mason, A., & Wilson, M. C. (2018) · Springer optimization and its applications · doi:10.1007/978-3-319-94830-0_3 · Cited by 14
Genome-wide discovery of missing genes in biological pathways of prokaryotes
Chen, Y., Mao, F., Li, G., & Xu, Y. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s1-s1 · Cited by 16
The distinctive signatures of promoter regions and operon junctions across prokaryotes
Janga, S. C., Lamboy, W. F., Huerta, A. M., & Moreno‐Hagelsieb, G. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl563 · Cited by 14
An event-driven approach for studying gene block evolution in bacteria
Ream, D. C., Bankapur, A. R., & Friedberg, I. (2015) · Bioinform. · doi:10.1093/bioinformatics/btv128 · Cited by 14

Authors: Salgado, H.
Affiliations: Universidad Nacional Autónoma de México (MX)
Corresponding author: Salgado, H.
ORCID: Salgado, H.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2006-01-01
Volume: 34
Issue: 90001
Pages: D394-D397
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkj156
PMC: PMC1347518
OpenAlex: W2146856779
Cited by: 368
References: 25
Citations by year: 2026: 3 · 2025: 8 · 2024: 7 · 2023: 2 · 2022: 1 · 2021: 7 · 2020: 4 · 2019: 9 · 2018: 3 · 2017: 3 · 2016: 14 · 2015: 11 · 2014: 14 · 2013: 11 · 2012: 16
FWCI: 28.22
Type: journal article
Language: en
Open access: gold
doi.org
Licence: other-oa
Locations: Nucleic Acids Research (publishedVersion, other-oa)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Figshare (submittedVersion, cc-by)
Figshare (cc-by)
Funders: National Institutes of Health
National Institute of General Medical Sciences (R01GM062205, GM62205-02)
National Center for Research Resources (1-R01-RR07861, R01RR007861)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords: RegulonDB, Escherichia coli K-12, transcriptional regulatory networks, operon organization, regulon, gene expression regulation, literature curation, EcoCyc, microarray comparison, functional gene networks
MeSH terms: Operon, Software, Transcription, Genetic, User-Computer Interface, Gene Expression Regulation, Bacterial, Genome, Bacterial, Regulon, Internet, Databases, Genetic, Escherichia coli K12

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks