Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence (Q34181401)

31 July 2017

Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence (English)

1 reference

31 July 2017

Staphylococcus aureus

1 reference

Dmitry A Ravcheev

1

1 reference

31 July 2017

Aaron A Best

2

1 reference

31 July 2017

Nathan Tintle

3

1 reference

31 July 2017

Matthew Dejongh

4

1 reference

31 July 2017

Andrei L Osterman

5

1 reference

31 July 2017

Pavel S Novichkov

6

1 reference

31 July 2017

Dmitry A Rodionov

7

1 reference

31 July 2017

language of work or name

English

0 references

publication date

29 April 2011

1 reference

31 July 2017

Journal of Bacteriology

1 reference

31 July 2017

193

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31 July 2017

13

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31 July 2017

3228-3240

1 reference

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

NCBI GEO: archive for functional genomics data sets--10 years on

5 July 2018

1 reference

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ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

SufD and SufC ATPase activity are required for iron acquisition during in vivo Fe-S cluster formation on SufB.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

5 July 2018

1 reference

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Accessing the SEED genome databases via Web services API: tools for programmers

5 July 2018

1 reference

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RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Iron-sulfur (Fe-S) cluster assembly: the SufBCD complex is a new type of Fe-S scaffold with a flavin redox cofactor.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Redox sensing by a Rex-family repressor is involved in the regulation of anaerobic gene expression in Staphylococcus aureus.

5 July 2018

1 reference

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Direct targets of CodY in Staphylococcus aureus.

5 July 2018

1 reference

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A novel role of malonyl-ACP in lipid homeostasis

5 July 2018

1 reference

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Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

MicrobesOnline: an integrated portal for comparative and functional genomics

5 July 2018

1 reference

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

At the crossroads of bacterial metabolism and virulence factor synthesis in Staphylococci

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Physiological proteomics and stress/starvation responses in Bacillus subtilis and Staphylococcus aureus.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Expression of the sarA family of genes in different strains of Staphylococcus aureus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Functional analysis of the Streptomyces coelicolor NrdR ATP-cone domain: role in nucleotide binding, oligomerization, and DNA interactions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Transcriptional regulation in bacterial membrane lipid synthesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Comparative genomic reconstruction of transcriptional regulatory networks in bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Evolution of transcriptional regulatory networks in microbial genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Global transcriptome analysis of Staphylococcus aureus response to hydrogen peroxide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

DBD: a transcription factor prediction database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Hydrogen peroxide increases the activities of soxRS regulon enzymes and the levels of oxidized proteins and lipids in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Uses of Staphylococcus aureus GeneChips in genotyping and genetic composition analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Autoinduction and signal transduction in the regulation of staphylococcal virulence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Missing genes in metabolic pathways: a comparative genomics approach

5 July 2018

1 reference

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Summaries of Affymetrix GeneChip probe level data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

PerR controls oxidative stress resistance and iron storage proteins and is required for virulence in Staphylococcus aureus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

The agr P2 operon: an autocatalytic sensory transduction system in Staphylococcus aureus.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Cloning, characterization, and sequencing of an accessory gene regulator (agr) in Staphylococcus aureus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Oxidative stress responses in Escherichia coli and Salmonella typhimurium

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Hydrogen peroxide sensing in Bacillus subtilis: it is all about the (metallo)regulator.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

SufE transfers sulfur from SufS to SufB for iron-sulfur cluster assembly.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Structural basis of lipid biosynthesis regulation in Gram-positive bacteria

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

FapR, a Bacterial Transcription Factor Involved in Global Regulation of Membrane Lipid Biosynthesis

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

Comparative genomics reveal novel heat shock regulatory mechanisms in Staphylococcus aureus and other Gram-positive bacteria.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

zur: a Zn(2+)-responsive regulatory element of Staphylococcus aureus.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3133287

[Software for analyzing bacterial genomes]

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21531804

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1128/JB.00350-11

1 reference

31 July 2017

1 reference

31 July 2017

1 reference