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Related Concept Videos

What is Cell Signaling?02:03

What is Cell Signaling?

Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate to respond to the environment.
What is Cell Signaling?02:03

What is Cell Signaling?

Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate to respond to the environment.
Cell-surface Signaling01:21

Cell-surface Signaling

Hormones—or any molecule that binds to a receptor, known as a ligand—that are lipid-insoluble (water-soluble) are not able to diffuse across the cell membrane. In order to be able to affect a cell without entering it, these hormones bind to receptors on the cell membrane. When a first messenger, a hormone, binds to a receptor, a signal cascade is set off, causing second messengers, proteins inside the cell, to become activated, resulting in downstream effects.
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 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.
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Overview of Cell-Matrix Interactions01:24

Overview of Cell-Matrix Interactions

The extracellular matrix or ECM holds cells together to form a tissue and allows the cells within the tissue to communicate. ECM comprises proteins such as fibronectin, collagen, laminin, etc. The most abundant protein in this space is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. ECM allows cell migration and provides a structural scaffold at cell adhesion that anchors the cell when the extracellular matrix proteins interact with...

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Related Experiment Video

Updated: May 19, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Narratives in the network: interactive methods for mining cell signaling networks.

M Shahriar Hossain1, Monika Akbar, Nicholas F Polys

  • 1Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24060, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|August 18, 2012
PubMed
Summary

This study introduces novel graph mining algorithms and a tool to uncover cellular signaling pathway relationships within the Signal Transduction Knowledge Environment (STKE). The approach enhances biological discovery by identifying pathway overlaps and connections.

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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Last Updated: May 19, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Published on: December 7, 2021

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Cellular signaling pathways are crucial for biological processes.
  • Understanding relationships between these pathways is complex.
  • Existing methods for pathway analysis have limitations.

Purpose of the Study:

  • To develop novel graph mining algorithms for analyzing cellular signaling pathways.
  • To create a graphical tool for biologists to discover pathway relationships.
  • To compare different data mining approaches for pathway analysis.

Main Methods:

  • Graph mining applied to the Signal Transduction Knowledge Environment (STKE) database.
  • Utilized clustering and storytelling approaches for pathway relationship discovery.
  • Developed a new subgraph discovery technique called Subgraph-Extension Generation (SEG).
  • Formulated pathway relationship discovery as a subgraph discovery problem.

Main Results:

  • The Subgraph-Extension Generation (SEG) technique significantly outperforms traditional Frequent Subgraph Discovery (FSG).
  • The developed tool facilitates the identification of similar pathways through clustering.
  • The storytelling approach reveals intermediate pathways, suggesting new hypotheses.
  • The tool allows comparison of different similarity measures and clustering techniques.

Conclusions:

  • The proposed graph mining approach and tool effectively identify relationships between cellular signaling pathways.
  • SEG offers a computationally efficient and powerful method for subgraph discovery in biological networks.
  • This work provides biologists with enhanced capabilities for hypothesis generation and experimental design.