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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,...
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Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Epistasis Analysis01:09

Epistasis Analysis

Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
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...

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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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Identifying gene interaction networks.

Gurkan Bebek1

  • 1Center for Proteomics and Bioinformatics, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA. gurkan@case.edu

Methods in Molecular Biology (Clifton, N.J.)
|February 7, 2012
PubMed
Summary
This summary is machine-generated.

This chapter introduces interaction networks, detailing their generation, storage, and sharing. It demonstrates using Cytoscape for network analysis and functional enrichment, applicable to larger biological datasets.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Network Science

Background:

  • Interaction networks are crucial for understanding complex biological systems.
  • Publicly available datasets offer valuable resources for network analysis.
  • Tools for network visualization and analysis are essential for researchers.

Purpose of the Study:

  • To introduce the generation, storage, and sharing of interaction networks.
  • To demonstrate a practical method for utilizing public interaction network data.
  • To analyze network topological features and functional enrichment.

Main Methods:

  • Utilized Cytoscape, an open-source network visualization and analysis tool.
  • Gathered and visualized a small interaction network.
  • Analyzed topological features and performed functional enrichment using Gene Ontology.
  • Integrated publicly available interaction network data.

Main Results:

  • Successfully gathered, visualized, and analyzed a small interaction network.
  • Identified topological features and performed functional enrichment of network nodes.
  • Demonstrated the utility of Cytoscape for network analysis.
  • Methods are scalable to larger, diverse biological networks.

Conclusions:

  • Publicly available interaction networks are valuable resources for biological research.
  • Cytoscape provides an accessible platform for network analysis and visualization.
  • The described methods facilitate the exploration of complex biological interactions and functions.