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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
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.
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,...
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.
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,...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
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...

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Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
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Published on: September 25, 2021

Extreme self-organization in networks constructed from gene expression data.

Himanshu Agrawal1

  • 1Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel. feagrawa@wicc.weizmann.ac.il

Physical Review Letters
|December 18, 2002
PubMed
Summary

This study reveals that gene networks in cancers exhibit power-law and small-world properties. Optimizing network homogeneity uncovers these complex structures, offering insights into cancer evolution.

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Area of Science:

  • Computational Biology
  • Network Science
  • Genomics

Background:

  • Gene expression data from various cancers are used to construct biological networks.
  • Network construction involves connecting genes based on K-nearest neighbor relationships.

Purpose of the Study:

  • To characterize the homogeneity of gene expression networks.
  • To identify underlying network structures and their properties in cancer data.
  • To explore the implications for evolutionary biological processes.

Main Methods:

  • Construction of gene networks using K-nearest neighbors from gene expression data.
  • Introduction of an order parameter to quantify network homogeneity.
  • Minimization of the order parameter to analyze network properties.
  • Analysis of eigenvalue spectrum to confirm network characteristics.

Main Results:

  • Network homogeneity is characterized by a novel order parameter.
  • Minimizing the order parameter reveals power-law degree distributions with an exponent of unity.
  • Eigenvalue spectrum analysis confirms both power-law and small-world network behaviors.

Conclusions:

  • Cancer gene networks exhibit complex topological features, including power-law and small-world characteristics.
  • The findings suggest these network properties may be linked to evolutionary biological processes in cancer.
  • This approach provides a framework for analyzing complex biological networks.