Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

You might also read

Related Articles

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

Sort by
Same author

On the translational potential of atlases in precision oncology.

Translational cancer research·2025
Same author

Paclitaxel neurotoxicity is triggered by epidermal EG5-dependent microtubule fasciculation and X-ROS formation.

Research square·2025
Same author

Can we cure antiphospholipid syndrome?

Current opinion in immunology·2025
Same author

Correction: The landscape of BRAF transcript and protein variants in human cancer.

Molecular cancer·2025
Same author

Health Professionals' Preferences for Next-Generation Sequencing in the Diagnosis of Suspected Genetic Disorders in the Paediatric Population.

Journal of personalized medicine·2025
Same author

Prioritizing Context-Dependent Cancer Gene Signatures in Networks.

Cancers·2025
Same journal

Correction to: A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice.

BMC systems biology·2019
Same journal

Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO.

BMC systems biology·2019
Same journal

Fusing gene expressions and transitive protein-protein interactions for inference of gene regulatory networks.

BMC systems biology·2019
Same journal

A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data.

BMC systems biology·2019
Same journal

GNE: a deep learning framework for gene network inference by aggregating biological information.

BMC systems biology·2019
Same journal

FCMDAP: using miRNA family and cluster information to improve the prediction accuracy of disease related miRNAs.

BMC systems biology·2019
See all related articles

Related Experiment Video

Updated: Jun 10, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Inferring modules from human protein interactome classes.

Elisabetta Marras1, Antonella Travaglione, Gautam Chaurasia

  • 1CRS4 Bioinformatics Laboratory-Technology Park of Sardinia, Pula (Cagliari), Sardinia, Italy.

BMC Systems Biology
|July 27, 2010
PubMed
Summary
This summary is machine-generated.

Integrating protein interaction data is crucial for systems biology. Analyzing disaggregated interactomes reveals modularity, enhancing network analysis and enabling confidence scoring for biological pathways.

More Related Videos

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

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Related Experiment Videos

Last Updated: Jun 10, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

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

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Area of Science:

  • Systems Biology
  • Network Analysis
  • Bioinformatics

Background:

  • Protein-protein interaction (PPI) networks are central to systems biology.
  • Integrating diverse PPI data sources is common but its impact on network analysis is understudied.
  • Optimizing data fusion requires considering coverage, accuracy, dependencies, and salient features.

Purpose of the Study:

  • To investigate the effects of integrating heterogeneous protein interaction datasets on network analysis outcomes.
  • To evaluate the utility of disaggregated interactomes versus integrated ones for inferring biological modules.
  • To develop a confidence scoring scheme for network modules.

Main Methods:

  • Applied network clustering methods to both integrated and disaggregated protein interaction data (interactome classes).
  • Focused on modularity analysis to identify potential protein complexes.
  • Validated extracted modules using Gene Ontology (GO), MIPS, and KEGG databases.
  • Combined protein interaction data with gene expression data for confidence scoring.

Main Results:

  • Disaggregated interactomes effectively inform modularity inference and contribute to integrative analysis.
  • Module validation using multiple annotations (GO, MIPS, KEGG) allows for confidence assessment.
  • A multilayer confidence scheme was proposed for network calibration, transitioning from unweighted to weighted interactomes.

Conclusions:

  • Disaggregated interactome data is valuable for understanding network modularity and improving integrative analyses.
  • The proposed confidence scheme enables robust assessment and calibration of protein interaction networks.
  • This approach facilitates a more accurate representation of biological pathways and protein complexes.