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Related Concept Videos

Protein Networks02:26

Protein Networks

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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 Complexes with Interchangeable Parts01:57

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Protein-protein Interfaces02:04

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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...
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Assembly of Complex Microtubule Structures01:32

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Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
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cytoHubba: identifying hub objects and sub-networks from complex interactome.

Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu

    BMC Systems Biology
    |December 19, 2014
    PubMed
    Summary

    CytoHubba is a Cytoscape plugin that ranks biological network nodes using 11 methods. Its Maximal Clique Centrality (MCC) method excels at identifying essential proteins in networks.

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    Area of Science:

    • Bioinformatics
    • Systems Biology
    • Network Biology

    Background:

    • Biological data, such as protein-protein interactions and gene regulations, are often represented as networks.
    • Analyzing network features helps infer node importance and identify central elements in biological systems.

    Purpose of the Study:

    • To introduce cytoHubba, a novel Cytoscape plugin for ranking nodes in biological networks based on network features.
    • To provide a user-friendly interface for exploring important nodes and facilitating new biological insights.

    Main Methods:

    • CytoHubba implements 11 distinct topological analysis methods for network node ranking.
    • These methods include Degree, Edge Percolated Component, Maximum Neighborhood Component, Density of Maximum Neighborhood Component, Maximal Clique Centrality (MCC), and six shortest-path-based centralities.

    Main Results:

    • CytoHubba offers a comprehensive suite of 11 network topological analysis methods within a single plugin.
    • The novel Maximal Clique Centrality (MCC) method demonstrated superior precision in identifying essential proteins within the yeast protein-protein interaction network.
    • The plugin has seen significant adoption, with approximately 6,700 downloads since 2010.

    Conclusions:

    • CytoHubba provides a user-friendly, integrated solution for identifying critical nodes in biological networks.
    • It enables researchers to combine topological analysis with other plugins for advanced analytical schemes.
    • The insights gained can guide experimental biologists toward novel regulatory networks and potential protein drug targets.