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Related Concept Videos

Global Regulatory Systems01:28

Global Regulatory Systems

Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Protein Networks02:26

Protein Networks

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IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and produces two-second...
Sequence Networks of Rotating Machines01:24

Sequence Networks of Rotating Machines

A Y-connected synchronous generator, grounded through a neutral impedance, is designed to produce balanced internal phase voltages with only positive-sequence components. The generator's sequence networks include a source voltage that is exclusively in the positive-sequence network. The sequence components of line-to-ground voltages at the generator terminals illustrate this configuration.
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...
Block Diagram Reduction01:22

Block Diagram Reduction

The process of deriving the transfer function of a control system often involves reducing its block diagram to a single block. This simplification can be achieved through a series of strategic operations, including relocating branch points and comparators. These operations preserve the overall function of the system while allowing for easier manipulation and combination of blocks.
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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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One hub-one process: a tool based view on regulatory network topology.

Jacob Bock Axelsen1, Sebastian Bernhardsson, Kim Sneppen

  • 1Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial, Ctra de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain. bockaj@inta.es

BMC Systems Biology
|March 6, 2008
PubMed
Summary

Molecular network topology in yeast reflects current cellular tasks rather than evolutionary history. Co-regulated proteins with similar functions cluster together, highlighting functional organization within regulatory networks.

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Area of Science:

  • Systems Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • The link between regulatory network design and molecular network function is crucial in biology.
  • Network modules and motifs are linked to cellular processes, suggesting performance-based localization.

Purpose of the Study:

  • To quantify the structure-function relationship in molecular networks.
  • To investigate protein similarities within the regulatory network of Saccharomyces Cerevisiae.

Main Methods:

  • Analysis of protein similarities based on proximity in the regulatory network.
  • Investigating topological features and their correlation with protein function.

Main Results:

  • Yeast regulatory network topology shows weak historical remnants but strong features of co-regulated proteins with similar tasks.
  • Functional correlations decrease significantly for proteins separated by more than two steps.
  • Network topology primarily reflects processes orchestrated by individual hubs, with minimal evidence of protein duplication history.

Conclusions:

  • Local topological features of regulatory networks arise implicitly from matching cellular processes to available proteins.
  • Broad degree distributions are an emergent property of this process-function matching.