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

4.6K
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,...
4.6K
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

7.6K
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...
7.6K
Diversity in Cell Signaling Responses01:22

Diversity in Cell Signaling Responses

8.2K
The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity. 
Graded and Abrupt Responses
Some signaling systems generate...
8.2K
Amplifying Signals via Enzymatic Cascade01:22

Amplifying Signals via Enzymatic Cascade

18.9K
When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze...
18.9K

You might also read

Related Articles

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

Sort by
Same author

Compositional Generative Model of Unbounded 4D Cities.

IEEE transactions on pattern analysis and machine intelligence·2025
Same author

Degradation of Bisphenol A by Nitrogen-Rich ZIF-8-Derived Carbon Materials-Activated Peroxymonosulfate.

Toxics·2024
Same author

Review of Drug Repositioning Approaches and Resources.

International journal of biological sciences·2018
Same author

Comparison among dimensionality reduction techniques based on Random Projection for cancer classification.

Computational biology and chemistry·2016
Same author

Network-based methods for identifying critical pathways of complex diseases: a survey.

Molecular bioSystems·2016
Same author

Extracellular calcium increases CXCR4 expression on bone marrow-derived cells and enhances pro-angiogenesis therapy.

Journal of cellular and molecular medicine·2009
Same journal

Research on multi-trait genome association study method based on Shannon information entropy.

BMC bioinformatics·2026
Same journal

A multi-view feature fusion framework with interpretable graph convolution for predicting microbe-drug associations.

BMC bioinformatics·2026
Same journal

Covariance decomposition for distance based species tree estimation.

BMC bioinformatics·2026
Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026
Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Mar 8, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.8K

A network-based pathway-expanding approach for pathway analysis.

Qiaosheng Zhang1,2, Jie Li3, Haozhe Xie1

  • 1School of Computer Science and Technology, Harbin Institute of Technology, West Da-Zhi Street, Harbin, China.

BMC Bioinformatics
|February 4, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces a novel network-based pathway-expanding approach to identify significant biological pathways for complex diseases. The method effectively analyzes gene interactions and pathway topology, improving disease pathogenesis insights.

Keywords:
Network-basedPathway analysisProtein-protein interactionSignificant pathway

More Related Videos

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

1.1K
A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

18.6K

Related Experiment Videos

Last Updated: Mar 8, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.8K
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

1.1K
A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

18.6K

Area of Science:

  • Systems biology
  • Computational biology
  • Genomics and proteomics

Background:

  • Pathway analysis integrating genomics and proteomics is crucial for understanding complex disease pathogenesis.
  • Existing methods often overlook interactions within and between biological pathways, presenting limitations.
  • A novel network-based approach is needed to address these challenges in pathway analysis.

Purpose of the Study:

  • To propose a network-based pathway-expanding approach that considers biological network topology.
  • To identify significant pathways involved in complex disease pathogenesis by analyzing gene interactions.
  • To overcome limitations of current pathway analysis methods.

Main Methods:

  • Construction of weighted gene-gene interaction networks (tumor and normal) using protein-protein interaction (PPI) data, gene expression, and pathway databases.
  • Identification of significant pathways by comparing topological structures of expanded pathways in weighted networks.
  • Application of the method to analyze breast cancer data and comparison with existing methods (GSEA, SPIA).

Main Results:

  • The proposed method successfully identified top pathways in breast cancer datasets, supported by biological literature.
  • The identified pathways showed significant differences in topological structures between tumor and normal networks.
  • Performance evaluation demonstrated the method's effectiveness compared to GSEA and SPIA.

Conclusions:

  • A novel network-based pathway-expanding approach effectively addresses limitations of existing pathway analysis.
  • The method accurately and reliably identifies disease-related significant pathways.
  • This approach enhances the understanding of complex disease pathogenesis through integrated network analysis.