Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network

BackgroundTranscriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs). However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined.ResultsBy studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs) do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect.ConclusionIndividual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.

• Publication year

  2004

• Venue

  BMC Bioinformatics

• Publication date

  2004-01-30

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-5-10PMID 15018656PMCID 357809
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Structure and function of the feed-forward loop network motif

  2003cited by this paper
• Feedback regulation in the lactose operon: a mathematical modeling study and comparison with experimental data.

  2003cited by this paper
• Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

  2003cited by this paper
• Motifs, modules and games in bacteria.

  2003cited by this paper
• Evolutionary conservation of motif constituents in the yeast protein interaction network

  2003cited by this paper
• The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks.

  2003cited by this paper
• Developmental gene regulatory network architecture across 500 million years of echinoderm evolution

  2003cited by this paper
• Detailed map of a cis-regulatory input function

  2003cited by this paper
• Convergent evolution of gene circuits

  2003influential reference
• On schemes of combinatorial transcription logic

  2003cited by this paper
• Deciphering gene expression regulatory networks.

  2002cited by this paper
• Specificity and Stability in Topology of Protein Networks

  2002cited by this paper
• Network motifs in the transcriptional regulation network of Escherichia coli

  2002influential reference
• Topological and causal structure of the yeast transcriptional regulatory network

  2002cited by this paper
• Negative autoregulation speeds the response times of transcription networks.

  2002cited by this paper
• Transcriptional Regulatory Networks in Saccharomyces cerevisiae

  2002cited by this paper
• Network motifs: simple building blocks of complex networks.

  2002influential reference
• Hierarchical Organization of Modularity in Metabolic Networks

  2002cited by this paper
• Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion

  2001cited by this paper
• Serial regulation of transcriptional regulators in the yeast cell cycle.

  2001cited by this paper
• RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12

  2001cited by this paper
• Error and attack tolerance of complex networks

  2000cited by this paper
• Engineering stability in gene networks by autoregulation

  2000cited by this paper
• From molecular to modular cell biology

  1999cited by this paper
• Emergence of scaling in random networks

  1999cited by this paper
• Emergence of Scaling in Random Networks

  1999cited by this paper
• From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli.

  1998cited by this paper

• Determining graphlet explanations for machine learning on graphs

  2025cites this paper
• Pesticide Residues Reduce Bacterial Diversity but Enhance Stability via Network Motif Restructuring

  2025cites this paper
• Topological communities in complex networks

  2024cites this paper
• GIDA MİKROBİYOLOJİSİ VE GENETİK: ESCHERICHIA COLI

  2024cites this paper
• PKI: A bioinformatics method of quantifying the importance of nodes in gene regulatory network via a pseudo knockout index.

  2023cites this paper
• Complexity reduction by symmetry: uncovering the minimal regulatory network for logical computation in bacteria

  2023cites this paper
• Complexity reduction by symmetry: Uncovering the minimal regulatory network for logical computation in bacteria

  2023cites this paper
• Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models

  2022cites this paper
• Exact and sampling methods for mining higher-order motifs in large hypergraphs

  2022cites this paper
• The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

  2022cites this paper
• Understanding the genome-wide transcription response to varying cAMP levels using phenomenological models in bacteria

  2022cites this paper
• The network perspective: Vertical connections linking organizational levels

  2022cites this paper
• Dynamical Modularity of the Genotype-Phenotype Map

  2021cites this paper
• Higher-order motif analysis in hypergraphs

  2021cites this paper
• Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

  2021cites this paper
• Discovery of network motifs based on induced subgraphs using a dynamic expansion tree

  2021cites this paper
• SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data

  2021cites this paper
• Systematic analysis of noise reduction properties of coupled and isolated feed-forward loops

  2021cites this paper
• Interplay between degree and Boolean rules in the stability of Boolean networks.

  2020cites this paper
• Review of tools and algorithms for network motif discovery in biological networks

  2020cites this paper
• Properties of the Vascular Networks in Malignant Tumors

  2020cites this paper
• NemoSuite: Web-based Network Motif Analytic Suite

  2020cites this paper
• NemoMapPy: Motif-centric network motif search on a web

  2019cites this paper
• Algorithms for Graph and Network Analysis: Clustering and Search of Motifs in Graphs

  2019cites this paper
• On the stability of multilayer Boolean networks under targeted immunization.

  2019cites this paper
• Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors

  2019cites this paper
• Condensed Graphs: Towards a General Approach for Faster Subgraph Census

  2019cites this paper
• Using of Network Motifs on Basketball Tactical Analysis

  2019cites this paper
• Optimal sparse network topology under sparse control in Laplacian networks

  2019cites this paper
• Sampling Methods for Counting Temporal Motifs

  2019cites this paper
• Developing machine learning tools to understand transcriptional regulation in plants

  2019cites this paper
• Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant

  2018cites this paper
• Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks

  2018cites this paper
• Subgraphs and motifs in a dynamic airline network

  2018cites this paper
• A sampling framework for counting temporal motifs

  2018cites this paper
• Network based Identification and Analysis of Structural Repeat Proteins

  2018cites this paper
• Understanding transcriptional regulation through computational analysis of single-cell transcriptomics

  2017cites this paper
• Organisation of feed-forward loop motifs reveals architectural principles in natural and engineered networks

  2017cites this paper
• NemoLib: A Java Library for Efficient Network Motif Detection

  2017cites this paper
• Characterizing regulatory path motifs in integrated networks using perturbational data

  2017cites this paper
• NemoProfile as an efficient approach to network motif analysis with instance collection

  2017cites this paper
• Animating and exploring phylogenies with fibre plots

  2017cites this paper
• Identification of regulatory modules in genome scale transcription regulatory networks

  2017cites this paper
• Bioinformatic analyses for T helper cell subtypes discrimination and gene regulatory network reconstruction

  2017cites this paper
• Crosstalk and the Dynamical Modularity of Feed-Forward Loops in Transcriptional Regulatory Networks

  2017cites this paper
• Optimal stabilization of Boolean networks through collective influence.

  2017cites this paper
• Graph Centrality Based Prediction of Cancer Genes

  2016cites this paper
• Triangle-Based Representative Possible Worlds of Uncertain Graphs

  2016cites this paper
• Higher-order organization of complex networks

  2016cites this paper
• A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

  2016cites this paper
• Large Scale Graph Representations for Subgraph Census

  2016cites this paper
• On Random SA-mixed Network Models Generated From Sierpinski and Apollonian networks

  2016cites this paper
• Cycle and flow trusses in directed networks

  2016cites this paper
• NemoProfile : Effective representation for network motif and their instances

  2016cites this paper
• MASS-Based NemoProfile Construction for an Efficient Network Motif Search

  2016cites this paper
• Efficient Communications in Wireless Sensor Networks Based on Biological Robustness

  2016cites this paper
• CeFunMO: A centrality based method for discovering functional motifs with application in biological networks

  2016cites this paper
• Finding Planted Subgraphs with Few Eigenvalues using the Schur-Horn Relaxation

  2016cites this paper
• Growing Network Models Having Part Edges Removed/added Randomly

  2015cites this paper
• A comparative study on network motif discovery algorithms

  2015cites this paper
• Improving microbial chemical production strains through transcriptional regulatory network rewiring

  2015cites this paper
• Sensible method for updating motif instances in an increased biological network.

  2015cites this paper
• Exploiting modularity and hierarchical modularity to infer large causal gene regulatory network

  2015cites this paper
• Gagg: A Graph Aggregation Operator

  2015cites this paper
• Networks of interactions between feed-forward loop transcriptional motifs in gene-regulatory networks

  2014cites this paper
• Fluctuation analysis in complex networks modeled by hidden-variable models: necessity of a large cutoff in hidden-variable models.

  2014cites this paper
• Network motifs that recur across species, including gene regulatory and protein–protein interaction networks

  2014cites this paper
• Efficient updates of network motif instances in the extended protein-protein interaction network

  2014cites this paper
• Molecular Networks – Representation and Analysis

  2014cites this paper
• Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network

  2014cites this paper
• Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns

  2014cites this paper
• Exploiting Gene Regulatory Networks for Robust Wireless Sensor Networking

  2014cites this paper
• ON THE USE AND FUTURE OF ALTERNATIVE TESTING STRATEGIES IN REGULATORY TOXICOLOGY

  2014influential citation
• The Epistemology of Causal Selection : Insights from Systems Biology

  2013cites this paper
• Topology Analysis of a Metabolic Functional Gene Transcriptional Regulatory Network of Escherichia Coli

  2013cites this paper
• The Index-Based Subgraph Matching Algorithm (ISMA): Fast Subgraph Enumeration in Large Networks Using Optimized Search Trees

  2013cites this paper
• Probabilistic Generation of Random Networks Taking into Account Information on Motifs Occurrence

  2013cites this paper
• Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis

  2013cites this paper
• Exploring network theory for mass drug administration.

  2013cites this paper
• Network analysis to model diseases and cellular reprogramming for therapeutic intervention

  2013cites this paper
• Boolean modeling of biological regulatory networks: a methodology tutorial.

  2013cites this paper
• Stability of Boolean networks: the joint effects of topology and update rules.

  2013cites this paper
• The Transcriptional Regulatory Network of Corynebacterium glutamicum

  2013cites this paper
• Network motifs provide signatures that characterize metabolism.

  2013cites this paper
• Corynebacterium glutamicum

  2013cites this paper
• Gene Coexpression as Hebbian Learning in Prokaryotic Genomes

  2013cites this paper
• Discovery and analysis of patterns in molecular networks: Link prediction, network analysis, and applications to novel drug target discovery

  2012cites this paper
• MotifsMotifs ingraphs inGraphsGraph motifs in

  2012cites this paper
• CytoKavosh: A Cytoscape Plug-In for Finding Network Motifs in Large Biological Networks

  2012cites this paper
• Innovative algorithms and evaluation methods for biological motif finding

  2012influential citation
• QSAR, Complex Networks, Principal Components and Partial Order Analysis of Drug Cardiotoxicity with Proteome Mass- Spectra Topological Indices

  2012cites this paper
• Interplay between gene expression noise and regulatory network architecture.

  2012cites this paper
• The interdisciplinary engineering knowledge genome

  2012cites this paper
• Biological network motif detection: principles and practice

  2012cites this paper
• Evolutionary Conservation and Network Structure Characterize Genes of Phenotypic Relevance for Mitosis in Human

  2012cites this paper
• Reconstruction And Analysis Of The Molecular Programs Involved In Deciding Mammalian Cell Fate

  2012cites this paper
• Network Motifs Provide Signatures That Characterize Metabolism and Produce Novel Insights into the Evolutionary History of the Eukaryotic Cell.

  2012cites this paper
• Data mining for microbiologists

  2012cites this paper
• The transcriptional regulatory network of Corynebacterium jeikeium K411 and its interaction with metabolic routes contributing to human body odor formation.

  2012cites this paper
• Motif Participation by Genes in E. coli Transcriptional Networks

  2012influential citation