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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,...
Protein-protein Interfaces02:04

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...
Protein-Protein Interfaces02:04

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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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...

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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

Visual integration of quantitative proteomic data, pathways, and protein interactions.

Radu Jianu1, Kebing Yu, Lulu Cao

  • 1Department of Computer Sciences, Brown University, Providence, RI 02912, USA. jr@cs.brown.edu

IEEE Transactions on Visualization and Computer Graphics
|May 15, 2010
PubMed
Summary

Novel visualization tools accelerate proteomic analysis by integrating protein-protein interaction networks with signaling pathways. This approach enhances understanding of complex biological systems and aids in making concrete discoveries.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein-protein interaction (PPI) networks and canonical signaling pathways are crucial for understanding cellular functions.
  • Analyzing large-scale quantitative proteomic data alongside these networks presents significant visualization and interaction challenges.
  • Existing methods may not fully leverage the interconnectedness of pathway models and experimental data for efficient analysis.

Purpose of the Study:

  • To introduce novel visualization and interaction paradigms for the analysis of PPI networks, signaling pathways, and proteomic data.
  • To demonstrate how these new methods can accelerate the process of proteomic data analysis.
  • To provide a prototype implementation for the proteomic community to evaluate.

Main Methods:

  • Development of new visualization techniques for PPI networks and signaling pathways.
  • Integration of quantitative proteomic data with network and pathway structures.
  • Anecdotal evaluation of the developed methods with domain scientists.

Main Results:

  • The proposed methods facilitate the structuring of PPI networks around canonical signaling pathways.
  • Simultaneous global and local exploration of pathways is enabled.
  • Analysis driven by experimental data accelerates the understanding of protein pathways.
  • Concrete discoveries were made in T-cells, mast cells, and the insulin signaling pathway.

Conclusions:

  • Integrating visualization of PPI networks with canonical signaling pathways accelerates proteomic analysis.
  • Driving analysis with experimental data is key to understanding complex protein pathways.
  • The developed visualization and interaction paradigms offer a valuable tool for the proteomic community.