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Related Concept Videos

Constitutive and Regulated Gene Expression01:27

Constitutive and Regulated Gene Expression

Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
Operon Model01:23

Operon Model

The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Protein Networks02:26

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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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
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Published on: August 16, 2017

Sample scale-free gene regulatory network using gene ontology.

Guanrao Chen1, Peter Larsen, Eyad Almasri

  • 1Department of Computer Science, University of Illinois at Chicago, IL 60607, USA. gchen4@uic.edu

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|October 20, 2007
PubMed
Summary

This study explores network sampling strategies to reconstruct scale-free gene regulatory networks. The goal is to improve network reconstruction by explicitly incorporating scale-free properties, a key feature of biological networks.

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Published on: May 31, 2011

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Gene regulatory networks (GRNs) are crucial for understanding cellular processes.
  • Existing GRN reconstruction methods often overlook the scale-free property inherent in biological networks.
  • Scale-free networks exhibit a hierarchical structure with highly connected hubs.

Purpose of the Study:

  • To develop and evaluate network sampling strategies for GRN reconstruction.
  • To explicitly incorporate the scale-free property into GRN reconstruction algorithms.
  • To improve the accuracy and biological relevance of reconstructed gene regulatory networks.

Main Methods:

  • Exploration of various network sampling strategies.
  • Application of strategies to a yeast gene interaction dataset.
  • Reconstruction of gene regulatory networks based on sampled data.

Main Results:

  • Evaluation of different sampling approaches for their effectiveness in capturing scale-free properties.
  • Identification of sampling strategies that best preserve the scale-free nature of the reconstructed networks.
  • Demonstration of improved network reconstruction by incorporating scale-free principles.

Conclusions:

  • Network sampling strategies can be effectively used to reconstruct scale-free gene regulatory networks.
  • Explicitly considering the scale-free property enhances the accuracy of GRN reconstruction.
  • This approach offers a promising direction for future systems biology research.