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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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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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Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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PathwayMatrix: visualizing binary relationships between proteins in biological pathways.

Tuan Nhon Dang1, Paul Murray1, Angus Graeme Forbes1

  • 1Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA.

BMC Proceedings
|September 12, 2015
PubMed
Summary
This summary is machine-generated.

PathwayMatrix is a new visualization tool that simplifies understanding complex molecular pathways. It uses an interactive matrix to display protein relationships, aiding researchers in pathway analysis.

Keywords:
Binary RelationshipsBiological networksMatrix visualizationPathway visualization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Molecular activation pathways are complex and difficult to analyze due to the vast number of biochemical reactions and diverse molecular relationships.
  • Visualizing and understanding large biological networks, including protein-protein interactions, presents significant challenges for researchers.

Purpose of the Study:

  • To introduce PathwayMatrix, an innovative visualization tool designed to simplify the analysis of molecular pathways.
  • To address the difficulties in understanding complex biological networks by providing an intuitive visualization method.

Main Methods:

  • PathwayMatrix utilizes an interactive adjacency matrix to represent binary relations between proteins within a pathway.
  • The tool incorporates features such as filtering, lensing, clustering, and brushing and linking for detailed protein analysis.

Main Results:

  • PathwayMatrix effectively visualizes protein-protein relationships in molecular pathways using an interactive adjacency matrix.
  • The implemented features allow for focused examination and analysis of specific proteins and their connections within a pathway.

Conclusions:

  • PathwayMatrix was positively evaluated by domain experts, indicating its potential utility for researchers.
  • The developed visualization technique offers a valuable approach for the broader scientific community engaged in pathway analysis.
  • PathwayMatrix is accessible for free use and further development at https://github.com/CreativeCodingLab/PathwayMatrix.