Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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,...

Proteomics

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Increasing value in the Veterans Affairs Healthcare System (VA) with precision health: a continuing landmark collaboration with the Department of Energy.

Journal of the American Medical Informatics Association : JAMIA·2026

Same author

Constitutive and inducible oleoresin defenses share genetic architectures and mechanisms in Pinus taeda.

The New phytologist·2026

Same author

Spatio-temporal dynamics of Hendra virus in Australia reveal stable maintenance of diverse viral clades among Pteropus bats.

Nature microbiology·2026

Same author

Metabolic flux, metabolite, and transcript analysis uncover reprogramming of metabolism toward higher seed oil.

Plant physiology·2026

Same author

A multi-layered approach to elucidate mechanisms of physical function in response to rehabilitation in heart failure with preserved ejection fraction.

medRxiv : the preprint server for health sciences·2026

Same author

A pennycress transparent testa 8 knockout mutant has drastic changes in seed coat anatomy and chemical compositions.

Journal of experimental botany·2026

Same journal

NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores For Single-Molecule Sensing.

GigaScience·2026

Same journal

From the Brain Cell Atlas to Precision Neurology: A review of the application of AI-driven multi-omics in brain science.

GigaScience·2026

Same journal

Comparison of Deep Learning Approaches for Extreme Low-SNR Image Restoration.

GigaScience·2026

Same journal

ScopeViewer: A Browser-Based Solution for Visualizing Large Biological Images.

GigaScience·2026

Same journal

ChatMDV: Reducing Technical Barriers in Bioinformatics Analysis using Large Language Models.

GigaScience·2026

Same journal

ClusterGraph: a new tool for visualisation and compression of multidimensional data.

GigaScience·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 10, 2025

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

RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species.

David Kainer^1,2, Matthew Lane^1,3, Kyle A Sullivan¹

¹Computational and Predictive Biology Group, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA.

|April 24, 2025

Summary

This summary is machine-generated.

RWRtoolkit is a new R package for exploring complex biological networks. It offers tools for analyzing relationships and evaluating connections within biological datasets, supporting high-throughput analysis.

Keywords:

multi-omic multiplex network random walk with restart software package systems biology

More Related Videos

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts

Published on: September 20, 2024

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Related Experiment Videos

Last Updated: May 10, 2025

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

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts

Published on: September 20, 2024

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Biological networks are crucial for understanding complex biological systems.
Analyzing large and intricate networks requires specialized computational tools.
Existing tools may lack the flexibility for custom datasets or high-throughput analysis.

Purpose of the Study:

Introduce RWRtoolkit, a novel package for R and command-line users.
Provide efficient tools for generating, exploring, and statistically analyzing multiplex biological networks.
Facilitate the analysis of custom and public biological datasets across species.

Main Methods:

Development of a software package (RWRtoolkit) for R and command-line environments.
Implementation of functions for topological distance calculation, relationship determination, and statistical evaluation within networks.
Design of a command-line interface for parallelization and high-throughput analysis, including permutation testing.
Integration of selected tools into the KBase web application for reproducible workflows.

Main Results:

RWRtoolkit enables efficient exploration of large, complex biological networks.
The package provides functions to analyze topological distances and relationships within biological entities.
Statistical evaluation of relationships within and between sets of interest is supported.
The command-line interface facilitates high-throughput analyses on cluster systems.

Conclusions:

RWRtoolkit offers a comprehensive solution for biological network analysis.
The package enhances the ability to uncover relationships and evaluate network properties.
Its design supports both custom data exploration and reproducible research workflows.