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Related Concept Videos

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,...
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.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
DNA Topoisomerases02:02

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types.  Type I...

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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

TopoGSA: network topological gene set analysis.

Enrico Glaab1, Anaïs Baudot, Natalio Krasnogor

  • 1School of Computer Science, Nottingham University, Nottingham, UK.

Bioinformatics (Oxford, England)
|March 26, 2010
PubMed
Summary
This summary is machine-generated.

TopoGSA (Topology-based Gene Set Analysis) offers a web application for analyzing gene and protein sets within molecular interaction networks. It computes and visualizes network topology, aiding in the comparison of biological pathways.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Molecular interaction networks are crucial for understanding cellular processes.
  • Analyzing gene and protein sets within these networks requires specialized tools.
  • Existing methods may not fully capture the topological significance of these sets.

Purpose of the Study:

  • To introduce TopoGSA (Topology-based Gene Set Analysis), a web application.
  • To enable computation and visualization of topological properties for gene and protein sets.
  • To facilitate comparison of these properties with known cellular pathways.

Main Methods:

  • Utilizes network topology analysis to assess gene and protein sets.
  • Computes various topological characteristics, including node centrality and clustering tendencies.
  • Visualizes network properties for intuitive interpretation.

Main Results:

  • TopoGSA provides a platform for in-depth analysis of molecular interaction networks.
  • Enables quantitative assessment of gene/protein set involvement in network topology.
  • Facilitates discovery of novel pathway associations through topological comparisons.

Conclusions:

  • TopoGSA enhances the analysis of gene and protein sets by integrating network topology.
  • The application aids researchers in understanding the structural roles of biological entities.
  • Offers a valuable tool for exploring and comparing cellular pathways and processes.