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,...
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and produces two-second...

You might also read

Related Articles

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

Sort by
Same author

ToxMet: a web tool for toxicogenomic data analysis using genome-scale metabolic modeling.

Toxicological sciences : an official journal of the Society of Toxicology·2026
Same author

Effect of exertion on the biomechanics of walking with load carriage and running in young, healthy women.

Scientific reports·2026
Same author

Cross-bridge model-based quantification of muscle metabolite alterations leading to fatigue during all-out knee extension exercise.

Frontiers in physiology·2026
Same author

A Case Study of AI-Enabled Software as a Medical Device Cleared by the FDA for Assessing Hemorrhage Risk Index (APPRAISE-HRI) after Trauma.

NEJM AI·2026
Same author

The changing face of dermatophytosis: from common skin disease to emerging resistant epidemic.

Clinical and experimental dermatology·2026
Same author

Post-kala-azar dermal leishmaniasis: a global overview.

Clinical and experimental dermatology·2026
Same journal

2DKD: a toolkit for content-based local image search.

Source code for biology and medicine·2020
Same journal

Computing and graphing probability values of pearson distributions: a SAS/IML macro.

Source code for biology and medicine·2020
Same journal

iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach.

Source code for biology and medicine·2019
Same journal

Social support for collaboration and group awareness in life science research teams.

Source code for biology and medicine·2019
Same journal

MZPAQ: a FASTQ data compression tool.

Source code for biology and medicine·2019
Same journal

IPCAPS: an R package for iterative pruning to capture population structure.

Source code for biology and medicine·2019
See all related articles

Related Experiment Video

Updated: May 18, 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

PathNet: a tool for pathway analysis using topological information.

Bhaskar Dutta1, Anders Wallqvist, Jaques Reifman

  • 1DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U,S, Army Medical Research and Materiel Command, Ft, Detrick, MD, 21702, USA. jaques.reifman@us.army.mil.

Source Code for Biology and Medicine
|September 26, 2012
PubMed
Summary
This summary is machine-generated.

PathNet, a new algorithm, analyzes gene expression data using pathway connectivity to reveal biological insights. It identified ubiquitin-mediated proteolysis pathway involvement in Alzheimer's disease, outperforming standard methods.

More Related Videos

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

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

Related Experiment Videos

Last Updated: May 18, 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

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

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

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • Canonical pathway enrichment is common for interpreting gene expression data.
  • Existing methods often overlook gene connectivity within and between pathways.
  • This limits the depth of biological insights derived from high-throughput studies.

Purpose of the Study:

  • To develop and validate PathNet, a novel algorithm for pathway analysis.
  • To leverage pathway connectivity information for enhanced interpretation of gene expression data.
  • To identify non-obvious dependencies and associations among biological pathways.

Main Methods:

  • PathNet algorithm development incorporating gene differential expression and pathway neighborhood information.
  • Utilizing topological information of gene interactions within and across canonical pathways.
  • Application of PathNet to Alzheimer's disease microarray datasets for performance comparison.

Main Results:

  • PathNet effectively identifies study-relevant pathways by considering gene connectivity.
  • The algorithm reveals complex biological relationships and dependencies among pathways.
  • PathNet highlighted the ubiquitin-mediated proteolysis pathway's role in Alzheimer's disease, missed by standard enrichment analyses.

Conclusions:

  • PathNet offers a novel approach to pathway enrichment and association analysis using gene expression data.
  • Incorporation of topological pathway information enhances biological discovery.
  • PathNet provides deeper biological insights beyond simple gene set enrichment.