Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach.

PubWeight™: 2.14‹?› | Rank: Top 2%

🔗 View Article (PMC 544888)

Published in BMC Bioinformatics on December 16, 2004

Authors

Hong-Wu Ma1, Jan Buer, An-Ping Zeng

Author Affiliations

1: Department of Genome Analysis, GBF - German Research Center for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany. hwm@gbf.de <hwm@gbf.de>

Articles citing this

Architecture of the human regulatory network derived from ENCODE data. Nature (2012) 10.28

Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol (2008) 4.57

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res (2004) 3.44

Advantages and limitations of current network inference methods. Nat Rev Microbiol (2010) 2.97

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci U S A (2005) 2.84

Toward the dynamic interactome: it's about time. Brief Bioinform (2010) 1.91

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol (2009) 1.73

Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc Natl Acad Sci U S A (2007) 1.64

The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response. BMC Syst Biol (2008) 1.36

A classification based framework for quantitative description of large-scale microarray data. Genome Biol (2006) 1.31

Biological role of noise encoded in a genetic network motif. Proc Natl Acad Sci U S A (2010) 1.25

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci U S A (2010) 1.24

CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics (2006) 1.24

Modular co-evolution of metabolic networks. BMC Bioinformatics (2007) 1.23

Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism. BMC Plant Biol (2008) 1.22

Hierarchy measure for complex networks. PLoS One (2012) 1.18

Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res (2008) 1.14

Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis. PLoS One (2010) 1.13

Transcriptional regulation shapes the organization of genes on bacterial chromosomes. Nucleic Acids Res (2009) 1.09

Robust detection of hierarchical communities from Escherichia coli gene expression data. PLoS Comput Biol (2012) 1.02

On the origins of hierarchy in complex networks. Proc Natl Acad Sci U S A (2013) 1.01

Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli. Nucleic Acids Res (2007) 0.93

Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach. Genome Biol (2008) 0.93

Bioreactor mixing efficiency modulates the activity of a prpoS::GFP reporter gene in E. coli. Microb Cell Fact (2009) 0.88

Evolution of transcriptional regulation in closely related bacteria. BMC Evol Biol (2012) 0.88

Dynamic changes in subgraph preference profiles of crucial transcription factors. PLoS Comput Biol (2006) 0.87

Evolution of gene regulatory networks by fluctuating selection and intrinsic constraints. PLoS Comput Biol (2010) 0.86

What determines the assembly of transcriptional network motifs in Escherichia coli? PLoS One (2008) 0.84

Extracting tag hierarchies. PLoS One (2013) 0.83

HiNO: an approach for inferring hierarchical organization from regulatory networks. PLoS One (2010) 0.82

Predicting cell cycle regulated genes by causal interactions. PLoS One (2009) 0.81

Profiling the transcription factor regulatory networks of human cell types. Nucleic Acids Res (2014) 0.80

An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. Genome Biol (2015) 0.79

Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. BMC Syst Biol (2009) 0.79

A Glimpse to Background and Characteristics of Major Molecular Biological Networks. Biomed Res Int (2015) 0.79

Random walk hierarchy measure: What is more hierarchical, a chain, a tree or a star? Sci Rep (2015) 0.79

Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton. BMC Genomics (2014) 0.78

Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks. PLoS Comput Biol (2015) 0.78

Hierarchical feedback modules and reaction hubs in cell signaling networks. PLoS One (2015) 0.76

Functional annotation of hierarchical modularity. PLoS One (2012) 0.76

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria. Database (Oxford) (2016) 0.75

The exact Laplacian spectrum for the Dyson hierarchical network. Sci Rep (2017) 0.75

Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast. BMC Syst Biol (2017) 0.75

Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach. Nucleic Acids Res (2010) 0.75

Comparing the Hierarchy of Keywords in On-Line News Portals. PLoS One (2016) 0.75

Hierarchical decomposition of dynamically evolving regulatory networks. BMC Bioinformatics (2015) 0.75

Global network structure of dominance hierarchy of ant workers. J R Soc Interface (2014) 0.75

Identification of key player genes in gene regulatory networks. BMC Syst Biol (2016) 0.75

Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades. Sci Rep (2015) 0.75

Articles cited by this

Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52

Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) 36.62

Network motifs: simple building blocks of complex networks. Science (2002) 35.80

TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26

From molecular to modular cell biology. Nature (1999) 23.51

Hierarchical organization of modularity in metabolic networks. Science (2002) 22.47

Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet (2002) 19.57

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56

EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res (2000) 9.67

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res (2003) 7.22

Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res (2004) 5.73

Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol (2003) 4.51

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics (2003) 4.49

Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48

Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet (2002) 4.22

The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. J Bacteriol (2000) 3.63

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A (2004) 3.49

Detection of functional modules from protein interaction networks. Proteins (2004) 3.08

Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res (2003) 2.87

The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics (2003) 2.73

Motifs, modules and games in bacteria. Curr Opin Microbiol (2003) 2.58

Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol (2004) 2.47

Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics (2004) 2.41

Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res (2003) 2.37

Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics (2002) 2.34

Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res (2003) 2.25

Convergent evolution of gene circuits. Nat Genet (2003) 1.89

Quantifying modularity in the evolution of biomolecular systems. Genome Res (2004) 1.67

Molecular networks: the top-down view. Science (2003) 1.65

Reconciling gene expression data with known genome-scale regulatory network structures. Genome Res (2003) 1.65

Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics (2004) 1.49

The modular era of functional genomics. Genome Biol (2003) 0.86

Articles by these authors

The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins. Nature (2008) 10.15

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol (2007) 7.58

Transforming growth factor-beta 'reprograms' the differentiation of T helper 2 cells and promotes an interleukin 9-producing subset. Nat Immunol (2008) 6.76

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol (2007) 6.21

Developmental stage, phenotype, and migration distinguish naive- and effector/memory-like CD4+ regulatory T cells. J Exp Med (2004) 5.08

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics (2003) 4.49

Cdkn1a deletion improves stem cell function and lifespan of mice with dysfunctional telomeres without accelerating cancer formation. Nat Genet (2006) 4.43

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res (2004) 3.44

A novel human primary immunodeficiency syndrome caused by deficiency of the endosomal adaptor protein p14. Nat Med (2006) 2.85

Neuropilin-1: a surface marker of regulatory T cells. Eur J Immunol (2004) 2.82

The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics (2003) 2.73

TLR13 recognizes bacterial 23S rRNA devoid of erythromycin resistance-forming modification. Science (2012) 2.66

Myeloid-derived suppressor cells in inflammatory bowel disease: a new immunoregulatory pathway. Gastroenterology (2008) 2.56

The Wingless homolog WNT5A and its receptor Frizzled-5 regulate inflammatory responses of human mononuclear cells induced by microbial stimulation. Blood (2006) 2.33

Purinergic control of T cell activation by ATP released through pannexin-1 hemichannels. Sci Signal (2008) 2.27

GATA-3 promotes maturation, IFN-gamma production, and liver-specific homing of NK cells. Immunity (2003) 2.15

Alveolar type II epithelial cells present antigen to CD4(+) T cells and induce Foxp3(+) regulatory T cells. Am J Respir Crit Care Med (2008) 2.15

Argyrin a reveals a critical role for the tumor suppressor protein p27(kip1) in mediating antitumor activities in response to proteasome inhibition. Cancer Cell (2008) 2.12

CX3CR1+ CD8alpha+ dendritic cells are a steady-state population related to plasmacytoid dendritic cells. Proc Natl Acad Sci U S A (2010) 1.94

Skp2-dependent degradation of p27kip1 is essential for cell cycle progression. Genes Dev (2004) 1.88

Probiotic Escherichia coli Nissle 1917 inhibits leaky gut by enhancing mucosal integrity. PLoS One (2007) 1.86

Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways. BMC Evol Biol (2004) 1.86

The Pseudomonas aeruginosa quinolone signal (PQS) has an iron-chelating activity. Environ Microbiol (2006) 1.70

Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J Bacteriol (2004) 1.63

Autoimmune-mediated intestinal inflammation-impact and regulation of antigen-specific CD8+ T cells. Gastroenterology (2006) 1.62

Gene expression profiling of human decidual macrophages: evidence for immunosuppressive phenotype. PLoS One (2008) 1.55

gamma(c) cytokines provide multiple homeostatic signals to naive CD4(+) T cells. Eur J Immunol (2007) 1.55

Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics (2004) 1.49

Quorum-sensing antagonistic activities of azithromycin in Pseudomonas aeruginosa PAO1: a global approach. Antimicrob Agents Chemother (2006) 1.46

Protein design and engineering of a de novo pathway for microbial production of 1,3-propanediol from glucose. Biotechnol J (2014) 1.45

Expression analysis of a highly adherent and cytotoxic small colony variant of Pseudomonas aeruginosa isolated from a lung of a patient with cystic fibrosis. J Bacteriol (2004) 1.43

Interleukin-6/glycoprotein 130-dependent pathways are protective during liver regeneration. J Biol Chem (2002) 1.42

Naive regulatory T cells: a novel subpopulation defined by resistance toward CD95L-mediated cell death. Blood (2006) 1.40

ATP inhibits the generation and function of regulatory T cells through the activation of purinergic P2X receptors. Sci Signal (2011) 1.38

Neuropilin 1 deficiency on CD4+Foxp3+ regulatory T cells impairs mouse melanoma growth. J Exp Med (2012) 1.38

G-CSF as immune regulator in T cells expressing the G-CSF receptor: implications for transplantation and autoimmune diseases. Blood (2003) 1.38

Common and unique gene expression signatures of human macrophages in response to four strains of Mycobacterium avium that differ in their growth and persistence characteristics. Infect Immun (2005) 1.29

On the edge of autoimmunity: T-cell stimulation by steady-state dendritic cells prevents autoimmune diabetes. Diabetes (2005) 1.29

Signatures of human regulatory T cells: an encounter with old friends and new players. Genome Biol (2006) 1.27

Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons. Environ Microbiol (2010) 1.24

The transcriptional repressor Gfi1 controls STAT3-dependent dendritic cell development and function. Immunity (2005) 1.22

Novel (2R,3R)-2,3-butanediol dehydrogenase from potential industrial strain Paenibacillus polymyxa ATCC 12321. Appl Environ Microbiol (2011) 1.21

Present state and perspective of downstream processing of biologically produced 1,3-propanediol and 2,3-butanediol. Appl Microbiol Biotechnol (2008) 1.21

Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp. Fungal Genet Biol (2009) 1.18

IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics (2004) 1.17

The cellular level of telomere dysfunction determines induction of senescence or apoptosis in vivo. EMBO Rep (2005) 1.16

Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives. J Biotechnol (2009) 1.15

Physiological responses of Pseudomonas aeruginosa PAO1 to oxidative stress in controlled microaerobic and aerobic cultures. Microbiology (2002) 1.14

Testing the importance of p27 degradation by the SCFskp2 pathway in murine models of lung and colon cancer. Proc Natl Acad Sci U S A (2006) 1.12

UBD, a downstream element of FOXP3, allows the identification of LGALS3, a new marker of human regulatory T cells. Lab Invest (2006) 1.12

Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data. J Biotechnol (2005) 1.11

Genome-wide transcriptional profiling of the steady-state response of Pseudomonas aeruginosa to hydrogen peroxide. J Bacteriol (2005) 1.10

The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate. Microb Cell Fact (2010) 1.10

Phylogenetic comparison of metabolic capacities of organisms at genome level. Mol Phylogenet Evol (2004) 1.09

Molecular and functional analysis of Shiga toxin-induced response patterns in human vascular endothelial cells. Blood (2003) 1.08

CD83 expression in CD4+ T cells modulates inflammation and autoimmunity. J Immunol (2008) 1.08

Cd14, Gbp1, and Pla2g2a: three major candidate genes for experimental IBD identified by combining QTL and microarray analyses. Physiol Genomics (2006) 1.08

Gene and protein characteristics reflect functional diversity of CD56dim and CD56bright NK cells. J Leukoc Biol (2006) 1.06

Iron deficiency leads to inhibition of oxygen transfer and enhanced formation of virulence factors in cultures of Pseudomonas aeruginosa PAO1. Microbiology (2003) 1.06

Nonfunctional regulatory T cells and defective control of Th2 cytokine production in natural scurfy mutant mice. J Immunol (2009) 1.06

G protein-coupled receptor 83 overexpression in naive CD4+CD25- T cells leads to the induction of Foxp3+ regulatory T cells in vivo. J Immunol (2006) 1.06

Resistance and susceptibility to tuberculosis analysed at the transcriptome level: lessons from mouse macrophages. Tuberculosis (Edinb) (2004) 1.04

Production of 1,3-propanediol by Clostridium butyricum growing on biodiesel-derived crude glycerol through a non-sterilized fermentation process. Appl Microbiol Biotechnol (2011) 1.04

Comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria. Biotechnol Prog (2003) 1.03

Expression of the quorum-sensing regulatory protein LasR is strongly affected by iron and oxygen concentrations in cultures of Pseudomonas aeruginosa irrespective of cell density. Microbiology (2005) 1.03

T cells, dendritic cells and epithelial cells in intestinal homeostasis. Int J Med Microbiol (2009) 1.03

CD4 T Lymphocyte-mediated lung disease: steady state between pathological and tolerogenic immune reactions. Am J Respir Crit Care Med (2004) 1.02

The host response to the probiotic Escherichia coli strain Nissle 1917: specific up-regulation of the proinflammatory chemokine MCP-1. BMC Med Genet (2005) 1.01

Intestinal immunity of Escherichia coli NISSLE 1917: a safe carrier for therapeutic molecules. FEMS Immunol Med Microbiol (2005) 0.99

GeneChip expression analysis of the VqsR regulon of Pseudomonas aeruginosa TB. FEMS Microbiol Lett (2005) 0.98

Phenotypic alterations in type II alveolar epithelial cells in CD4+ T cell mediated lung inflammation. Respir Res (2007) 0.98

Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Biotechnol Bioeng (2003) 0.97

Comparison of a shiga toxin enzyme-linked immunosorbent assay and two types of PCR for detection of shiga toxin-producing Escherichia coli in human stool specimens. J Clin Microbiol (2003) 0.96

Quantification of regulatory T cells in septic patients by real-time PCR-based methylation assay and flow cytometry. PLoS One (2012) 0.96

Nonlinear dynamics of regulation of bacterial trp operon: model analysis of integrated effects of repression, feedback inhibition, and attenuation. Biotechnol Prog (2002) 0.95

Analysis of Cd14 as a genetic modifier of experimental inflammatory bowel disease (IBD) in mice. Inflamm Bowel Dis (2009) 0.94

Coevolutionary analysis enabled rational deregulation of allosteric enzyme inhibition in Corynebacterium glutamicum for lysine production. Appl Environ Microbiol (2011) 0.94

Genes for the majority of group a streptococcal virulence factors and extracellular surface proteins do not confer an increased propensity to cause invasive disease. Clin Infect Dis (2006) 0.93

Essential role of CCL2 in clustering of splenic ERTR-9+ macrophages during infection of BALB/c mice by Listeria monocytogenes. Infect Immun (2006) 0.93

Gene expression signatures of peripheral CD4+ T cells clearly discriminate between patients with acute and chronic hepatitis B infection. Hepatology (2009) 0.93

In search of functional association from time-series microarray data based on the change trend and level of gene expression. BMC Bioinformatics (2006) 0.93

Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions. Bioprocess Biosyst Eng (2009) 0.93

Genetically induced pancreatic adenocarcinoma is highly immunogenic and causes spontaneous tumor-specific immune responses. Cancer Res (2006) 0.93

Strong impact of CD4+ Foxp3+ regulatory T cells and limited effect of T cell-derived IL-10 on pathogen clearance during Plasmodium yoelii infection. J Immunol (2012) 0.93

Functional characterization of the gene PA2384 in large-scale gene regulation in response to iron starvation in Pseudomonas aeruginosa. J Biotechnol (2007) 0.92

A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains. BMC Genomics (2012) 0.92

Integrating molecular dynamics and co-evolutionary analysis for reliable target prediction and deregulation of the allosteric inhibition of aspartokinase for amino acid production. J Biotechnol (2011) 0.91

Gene expression profile at the G1/S transition of liver regeneration after partial hepatectomy in mice. Cell Cycle (2004) 0.91

Efficient production of 1,3-propanediol from fermentation of crude glycerol with mixed cultures in a simple medium. Bioprocess Biosyst Eng (2013) 0.91

Direct identification of bacteria in urine samples by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and relevance of defensins as interfering factors. J Med Microbiol (2012) 0.91

Identification of unique gene expression patterns within different lesional sites of keloids. Wound Repair Regen (2008) 0.91

Multiplex PCR for rapid and improved diagnosis of bloodstream infections in liver transplant recipients. J Clin Microbiol (2012) 0.90

CD4+CD25+Foxp3+ regulatory T cells are dispensable for controlling CD8+ T cell-mediated lung inflammation. J Immunol (2011) 0.90

FOXP3 and GARP (LRRC32): the master and its minion. Biol Direct (2010) 0.90

The use of calcium phosphate nanoparticles encapsulating Toll-like receptor ligands and the antigen hemagglutinin to induce dendritic cell maturation and T cell activation. Biomaterials (2010) 0.89

PLAU inferred from a correlation network is critical for suppressor function of regulatory T cells. Mol Syst Biol (2012) 0.89

Enhanced 1,3-propanediol production by a newly isolated Citrobacter freundii strain cultivated on biodiesel-derived waste glycerol through sterile and non-sterile bioprocesses. J Biotechnol (2012) 0.88

A population balance model describing the cell cycle dynamics of myeloma cell cultivation. Biotechnol Prog (2007) 0.88