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Updated: Oct 26, 2025

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Paths Through the Yeast Regulatory Network in Different Physiological States.

Arthur M Lesk1, Arun S Konagurthu2

  • 1Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

Journal of Molecular Biology
|August 2, 2021
PubMed
Summary

Yeast gene regulation networks share components but form distinct paths across physiological states. The cell-cycle network uniquely exhibits a high proportion of source-to-sink paths.

Keywords:
pathway analysis and comparisonregulatory networkssystems biology

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Molecular Biology

Background:

  • Gene-expression patterns are controlled by complex regulatory networks.
  • These networks dynamically reconfigure across different physiological states.
  • Understanding network structure and function is crucial for deciphering cellular processes.

Purpose of the Study:

  • To analyze and compare paths within yeast regulatory networks across five physiological states.
  • To investigate the sharing of nodes and edges among these networks.
  • To identify how different network structures facilitate distinct functional pathways.

Main Methods:

  • Analysis of directed graphs representing regulatory networks in yeast.
  • Identification of source and sink nodes within each network.
  • Enumeration and comparison of paths between source and sink nodes across states.

Main Results:

  • Yeast regulatory networks exhibit substantial sharing of nodes and edges.
  • Despite shared components, networks assemble into distinct sets of paths.
  • The cell-cycle network is an outlier, possessing a significantly higher proportion of source-to-sink paths compared to other states.

Conclusions:

  • Regulatory networks are modular, reusing components but creating unique pathway configurations.
  • The cell-cycle network's distinct path structure suggests specialized regulatory mechanisms.
  • Comparative network analysis provides insights into state-specific gene regulation.