A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0
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Title
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0
Authors
Keywords
Transcriptional regulation, Transcriptomics, Integrative analyses, Systems biology, ChIP-seq, gSELEX
Journal
BMC BIOLOGY
Volume 16, Issue 1, Pages -
Publisher
Springer Nature America, Inc
Online
2018-08-16
DOI
10.1186/s12915-018-0555-y
References
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Note: Only part of the references are listed.- Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
- (2017) Sang Woo Seo et al. Scientific Reports
- The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12
- (2016) Ingrid M. Keseler et al. NUCLEIC ACIDS RESEARCH
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- (2015) Tomohiro Shimada et al. GENES TO CELLS
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- (2015) Kaneyoshi Yamamoto et al. MICROBIOLOGY-SGM
- COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses: Table 1.
- (2015) Marco Moretto et al. NUCLEIC ACIDS RESEARCH
- The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli
- (2015) Suhyung Cho et al. NUCLEIC ACIDS RESEARCH
- RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
- (2015) Socorro Gama-Castro et al. NUCLEIC ACIDS RESEARCH
- Impact of Anaerobiosis on Expression of the Iron-Responsive Fur and RyhB Regulons
- (2015) Nicole A. Beauchene et al. mBio
- Characterization of the Escherichia coli σS core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis
- (2015) Clelia Peano et al. Scientific Reports
- Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems
- (2015) Tesfalem R. Zere et al. PLoS One
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- (2014) Tomohiro Shimada et al. GENES TO CELLS
- Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
- (2014) Antonio L.C. Gomes et al. GENOME RESEARCH
- Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli
- (2014) Maureen K. Thomason et al. JOURNAL OF BACTERIOLOGY
- ArrayExpress update—simplifying data submissions
- (2014) Nikolay Kolesnikov et al. NUCLEIC ACIDS RESEARCH
- STRING v10: protein–protein interaction networks, integrated over the tree of life
- (2014) Damian Szklarczyk et al. NUCLEIC ACIDS RESEARCH
- Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
- (2014) Sang Woo Seo et al. Nature Communications
- Determining the Control Circuitry of Redox Metabolism at the Genome-Scale
- (2014) Stephen Federowicz et al. PLoS Genetics
- Novel regulator PgrR for switch control of peptidoglycan recycling inEscherichia coli
- (2013) Tomohiro Shimada et al. GENES TO CELLS
- Evidence classification of high-throughput protocols and confidence integration in RegulonDB
- (2013) Verena Weiss et al. Database-The Journal of Biological Databases and Curation
- Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding
- (2013) Kevin S. Myers et al. PLoS Genetics
- Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli
- (2012) H. Ogasawara et al. MICROBIOLOGY-SGM
- RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
- (2012) Heladia Salgado et al. NUCLEIC ACIDS RESEARCH
- A novel regulator RcdA of thecsgDgene encoding the master regulator of biofilm formation inEscherichia coli
- (2012) Tomohiro Shimada et al. MicrobiologyOpen
- Role of the Biofilm Master Regulator CsgD in Cross-Regulation between Biofilm Formation and Flagellar Synthesis
- (2011) H. Ogasawara et al. JOURNAL OF BACTERIOLOGY
- Theoretical and empirical quality assessment of transcription factor-binding motifs
- (2011) Alejandra Medina-Rivera et al. NUCLEIC ACIDS RESEARCH
- ChIP on Chip: surprising results are often artifacts
- (2010) Torsten Waldminghaus et al. BMC GENOMICS
- Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli
- (2010) T. Shimada et al. JOURNAL OF BACTERIOLOGY
- Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli
- (2010) Christina Kahramanoglou et al. NUCLEIC ACIDS RESEARCH
- A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions
- (2010) Jun Teramoto et al. NUCLEIC ACIDS RESEARCH
- Involvement of the Leucine Response Transcription Factor LeuO in Regulation of the Genes for Sulfa Drug Efflux
- (2009) T. Shimada et al. JOURNAL OF BACTERIOLOGY
- Participation of Regulator AscG of the -Glucoside Utilization Operon in Regulation of the Propionate Catabolism Operon
- (2009) Y. Ishida et al. JOURNAL OF BACTERIOLOGY
- NsrR targets in theEscherichia coligenome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility
- (2009) Jonathan D. Partridge et al. MOLECULAR MICROBIOLOGY
- Rho directs widespread termination of intragenic and stable RNA transcription
- (2009) J. M. Peters et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
- (2009) Desmond S Lun et al. GENOME BIOLOGY
- Anaerobic Regulation of Citrate Fermentation by CitAB inEscherichia coli
- (2008) Kaneyoshi YAMAMOTO et al. BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
- The Uncharacterized Transcription Factor YdhM Is the Regulator of the nemA Gene, Encoding N-Ethylmaleimide Reductase
- (2008) Y. Umezawa et al. JOURNAL OF BACTERIOLOGY
- The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
- (2008) Tomohiro Shimada et al. NUCLEIC ACIDS RESEARCH
- Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli
- (2008) B.-K. Cho et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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