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Protein Networks

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 Networks

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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Related Experiment Video

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

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

Published on: October 19, 2021

Network Analysis Tools: from biological networks to clusters and pathways.

Sylvain Brohée¹, Karoline Faust, Gipsi Lima-Mendez

¹Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium.

Nature Protocols

|September 20, 2008

Summary

Network Analysis Tools (NeAT) offers integrated algorithms for biological network analysis, enabling efficient exploration of protein-protein interactions and other complex networks within minutes.

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Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Biological networks, such as protein-protein interaction networks, are crucial for understanding cellular mechanisms.
Analyzing these complex networks requires sophisticated computational tools capable of handling large datasets.

Purpose of the Study:

To present Network Analysis Tools (NeAT), a suite of integrated algorithms for comprehensive biological network analysis.
To demonstrate a typical workflow using NeAT for deciphering protein-protein interaction networks.

Main Methods:

NeAT integrates algorithms for graph and cluster comparison, network randomization, degree distribution analysis, clustering, and path finding.
A stepwise analytical workflow allows for interconnected analysis of biological networks.
The protocol details the utilization of NeAT on a protein-protein interaction network from the STRING database.

Main Results:

NeAT provides results such as subnetworks, enriched networks (clusters, paths), and statistical tables.
The tools efficiently analyze large networks (thousands of nodes and arcs) in minutes.
A complete analytical protocol can be executed in approximately one hour.

Conclusions:

NeAT offers a powerful and efficient solution for the analysis of complex biological networks.
The integrated approach within NeAT facilitates a thorough understanding of network properties and biological insights.
This protocol provides a practical guide for researchers to leverage NeAT for network-based biological discovery.