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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.
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Vectors can be multiplied by scalars, added to other vectors, or subtracted from other vectors. The vector sum of two (or more) vectors is called the resultant vector or, for short, the resultant.
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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...
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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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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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BENviewer: a gene interaction network visualization server based on graph embedding model.

Yunqing Liu1, Yunchi Zhu1, Chunpeng He1

  • 1State Key Laboratory of Bioelectronics, Southeast University, Sipailou No.2, Nanjing, Jiangsu 210096, China.

Database : the Journal of Biological Databases and Curation
|May 28, 2021
PubMed
Summary
This summary is machine-generated.

BENviewer is a new online tool that visualizes gene interaction networks using graph embedding. This server offers intuitive 2D pathway visualizations to help researchers explore biological networks more deeply.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Gene interaction networks are crucial for understanding biological processes.
  • Existing visualization tools may not fully capture the complexity of these networks.
  • Graph embedding models offer a novel approach to network analysis.

Purpose of the Study:

  • To introduce BENviewer, a novel online server for gene interaction network visualization.
  • To leverage graph embedding techniques for enhanced biological network analysis.
  • To provide researchers with an intuitive platform for exploring gene interactions and pathway data.

Main Methods:

  • Application of mature graph embedding algorithms to interaction network databases.
  • Development of a user-friendly 2D visualization server.
  • Integration of over 2000 biological pathways into the visualization framework.
  • URL optimization for batch data acquisition.

Main Results:

  • BENviewer provides intuitive 2D visualizations of gene interaction networks.
  • Visualizations highlight involved genes and the tightness of their interactions.
  • The server uniquely applies graph embedding for biological network exploration.
  • Simplified user operation flow and batch data acquisition capabilities.

Conclusions:

  • BENviewer offers a novel approach to visualizing gene interaction networks using graph embedding.
  • The tool facilitates deeper insights into biological networks beyond current knowledge.
  • BENviewer is freely available and open-sourced, promoting wider research accessibility.