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

Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

6.3K
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...
6.3K
Protein Networks02:26

Protein Networks

4.0K
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,...
4.0K
Epistasis Analysis01:09

Epistasis Analysis

5.0K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
5.0K
Biostatistics: Overview01:20

Biostatistics: Overview

246
Biostatistics plays a crucial role in understanding and analyzing data in healthcare and biology. Biostatisticians conduct experiments, gather evidence, and draw meaningful conclusions using statistical methods and techniques. Different variables form the foundation of biostatistical analysis, allowing researchers to understand and interpret data effectively. These variables are classified into different types, each serving a specific purpose in statistical analysis.
Discrete variables are...
246
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K

You might also read

Related Articles

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

Sort by
Same author

CycleVI: isolating cell cycle variation with an interpretable deep generative model.

Bioinformatics (Oxford, England)·2026
Same author

Better Inputs, Better Learning: A Peptide Embedding Tutorial for Proteomic Mass Spectrometry.

Journal of proteome research·2026
Same author

Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra.

Journal of proteome research·2025
Same author

Open-Source and FAIR Research Software for Proteomics.

Journal of proteome research·2025
Same author

Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI.

Analytical chemistry·2025
Same author

How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate.

Journal of proteome research·2025

Related Experiment Video

Updated: Jul 6, 2025

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

3.3K

Pathway analysis through mutual information.

Gustavo S Jeuken1,2, Lukas Käll1

  • 1Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm 171 65, Sweden.

Bioinformatics (Oxford, England)
|January 10, 2024
PubMed
Summary

We introduce MIPath, a novel pathway analysis method using information theory. MIPath offers a robust and scalable approach for single-cell data, avoiding linear assumptions and improving reproducibility.

More Related Videos

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

1.1K
Methods to Study Mrp4-containing Macromolecular Complexes in the Regulation of Fibroblast Migration
10:43

Methods to Study Mrp4-containing Macromolecular Complexes in the Regulation of Fibroblast Migration

Published on: May 19, 2016

6.8K

Related Experiment Videos

Last Updated: Jul 6, 2025

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

3.3K
Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

1.1K
Methods to Study Mrp4-containing Macromolecular Complexes in the Regulation of Fibroblast Migration
10:43

Methods to Study Mrp4-containing Macromolecular Complexes in the Regulation of Fibroblast Migration

Published on: May 19, 2016

6.8K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Pathway analysis connects biological pathway activity to phenotypic differences.
  • Existing methods often use differential expression analysis and linear models.
  • These approaches can be limited by assumptions and vulnerability to missing data.

Purpose of the Study:

  • Propose MIPath, a new information-theoretic pathway analysis method.
  • Develop a scalable and assumption-light approach for biological data.
  • Enhance pathway analysis for single-cell omics data.

Main Methods:

  • Utilize information-theoretic principles, specifically Mutual Information.
  • Construct pathway data point graphs using a nearest-neighbor approach.
  • Score phenotype-pathway associations while adjusting for random chance.

Main Results:

  • MIPath demonstrates robustness and reproducibility across single-cell datasets.
  • The method is scalable and less susceptible to missing values.
  • MIPath provides meaningful pathway activity scores compared to existing methods.

Conclusions:

  • MIPath offers a powerful new tool for pathway analysis, especially for single-cell data.
  • Its information-theoretic foundation reduces reliance on restrictive modeling assumptions.
  • The method enhances the understanding of biological pathways and their relation to phenotypes.