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 Experiment Videos

Extracting three-way gene interactions from microarray data.

Jiexin Zhang1, Yuan Ji, Li Zhang

  • 1Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030-4009, USA.

Bioinformatics (Oxford, England)
|October 9, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Insights into semaglutide cardiovascular research: Mechanisms, trials, and frontiers.

European journal of pharmacology·2026
Same author

Multi-Head Attention Deep Q-Network with Prioritized Experience Replay for UAV Path Planning in Dynamic Environments: A Bio-Inspired Approach.

Biomimetics (Basel, Switzerland)·2026
Same author

A novel Sinomonas strain and Its genus-wide genomic insights into plant growth-promoting potential.

BMC microbiology·2026
Same author

NOTCH1 acts as a tumor suppressor that induces early differentiation in head and neck cancer.

JCI insight·2026
Same author

Compound 17 Inhibits Lung Cancer Progression via Inducing Cellular Apoptosis and Blocking TNF Signaling Pathway Activation.

International journal of molecular sciences·2026
Same author

Prognostic impact of disc perforation on condylar remodeling following temporomandibular joint disc repositioning surgery in adult patients with ADDWoR: a single-center cohort study.

Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery·2025
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles

This study introduces a novel three-way gene interaction model to uncover complex gene networks beyond simple pairwise correlations. The model identifies gene triplets where a third gene dynamically controls the co-expression or mutual exclusivity of two other genes, offering new avenues for biological pathway discovery.

Area of Science:

  • Genomics
  • Systems Biology
  • Bioinformatics

Background:

  • Extracting gene network information from high-throughput genomic data is challenging.
  • Pairwise correlation is a simplistic metric for complex gene relationships, often limited by biological conditions.
  • A dynamic, condition-specific approach is needed to accurately model gene co-expression.

Purpose of the Study:

  • To develop and validate a three-way gene interaction model.
  • To capture the dynamic nature of gene co-expression relationships.
  • To identify novel gene networks and pathways.

Main Methods:

  • Surveyed 0.4 billion three-way interactions among 1000 genes using a microarray dataset.
  • Utilized a training and testing set split for reproducibility and statistical significance testing.

Related Experiment Videos

  • Applied appropriate statistical tests to identify significant gene triplets.

    • Main Results:

    • Identified reproducible three-way gene interactions with high statistical significance.
    • Discovered a pattern where a controller gene dictates co-expression or mutual exclusivity of two other genes.
    • Found that these three-way interactions can exist independently of pairwise correlations.

    Conclusions:

    • The three-way gene interaction model provides a more nuanced understanding of gene networks.
    • Identified gene triplets serve as candidates for further experimental validation (e.g., RNA interference).
    • This approach facilitates the discovery of novel gene networks and biological pathways.