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,...

Protein-protein Interfaces

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...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

Interactions Between Signaling Pathways

Interactions Between Signaling Pathways

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...

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

You might also read

Related Articles

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

Sort by

Same author

Incremental prognostic value of coronary artery calcium progression within a large community-benefit calcium score registry.

American journal of preventive cardiology·2026

Same author

Combining cutting edge computational and experimental methods for targeting KRAS mutations in non-small cell lung cancer.

Expert opinion on drug discovery·2026

Same author

Multiscale analysis and optimal glioma therapeutic candidate discovery using the CANDO platform.

Journal of cheminformatics·2026

Same author

Uncovering novel therapeutics for schizophrenia: a multitarget approach using the CANDO platform.

bioRxiv : the preprint server for biology·2026

Same author

Cardiac MR Fingerprinting at 0.55T Using a Deep Image Prior for Joint T<sub>1</sub>, T<sub>2</sub>, and M<sub>0</sub> Mapping.

Journal of magnetic resonance imaging : JMRI·2026

Same author

Myocarditis Mimicking Takotsubo Cardiomyopathy With First Dose of Neoadjuvant Nivolumab-Relatlimab.

Case reports in oncological medicine·2025

Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Videos

Inferring molecular interactions pathways from eQTL data.

Imran Rashid¹, Jason McDermott, Ram Samudrala

¹Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|April 22, 2009

Summary

This summary is machine-generated.

This study introduces novel methods to identify specific genes and molecular pathways driving gene expression changes identified through expression quantitative trait loci (eQTL) analysis, improving our understanding of genotype-phenotype links.

Related Experiment Videos

Area of Science:

Genetics
Systems Biology
Bioinformatics

Background:

Expression quantitative trait loci (eQTL) analysis links genomic loci to gene expression but struggles to pinpoint causal genes.
Identifying specific genes and molecular pathways underlying eQTL effects is a significant challenge in genetic research.
Standard methods lack the resolution to determine which gene within a locus controls expression levels or the responsible molecular interactions.

Purpose of the Study:

To develop and present techniques for identifying specific genes and molecular pathways that explain differential gene expression in eQTL data.
To overcome the limitations of standard statistical genetics in pinpointing causal genes and interaction pathways within genomic loci.
To provide a framework for exploring molecular interaction graphs to understand the mechanisms of gene regulation.

Main Methods:

Utilizing graphs of molecular interactions to explore and identify regulatory pathways.
Developing and applying a series of novel techniques for pathway discovery.
Analyzing eQTL data to find explanatory pathways for differential expression.

Main Results:

Demonstrated the ability of the described techniques to find complete pathways explaining differential expression.
Showcased simple methods capable of identifying the specific genes and molecular interactions involved in eQTL.
Successfully linked genomic loci effects to specific genes and their regulatory networks.

Conclusions:

The developed methods effectively identify specific genes and molecular pathways responsible for expression changes observed in eQTL studies.
Exploring molecular interaction graphs provides a powerful approach to elucidate the mechanisms of gene regulation and genotype-phenotype relationships.
These techniques offer a significant advancement in understanding the genetic architecture of complex traits by resolving gene-level effects within eQTL loci.