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

Operon Model01:23

Operon Model

886
The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
886
Protein Networks02:26

Protein Networks

4.4K
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,...
4.4K

You might also read

Related Articles

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

Sort by
Same author

Mucin-induced metabolic reprogramming in <i>Pseudomonas aeruginosa</i> clinical isolates.

mSystems·2026
Same author

Environmental former <i>Massilia</i> group bacteria secrete metabolites that promote <i>Leptospira</i> growth.

mSystems·2026
Same author

Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics.

Nature microbiology·2026
Same author

Monotherapy cancer drug-blind response prediction is limited to intraclass generalization.

PLoS computational biology·2026
Same author

Enzyme-enhanced RNA isolation from biofilm-producing bacteria.

Microbiology spectrum·2026
Same author

Metabolic network analysis of Crohn's disease reveals sex- and age-specific cellular phenotypes.

Cell systems·2026

Related Experiment Video

Updated: Dec 21, 2025

Author Spotlight: Emerging Technologies and Advanced Tools for Decoding Metabolomics Data Analysis
07:11

Author Spotlight: Emerging Technologies and Advanced Tools for Decoding Metabolomics Data Analysis

Published on: November 10, 2023

3.1K

Functional integration of a metabolic network model and expression data without arbitrary thresholding.

Paul A Jensen1, Jason A Papin

  • 1Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA.

Bioinformatics (Oxford, England)
|December 22, 2010
PubMed
Summary
This summary is machine-generated.

Metabolic Adjustment by Differential Expression (MADE) maps gene expression data to metabolic models without arbitrary thresholds. This method accurately reflects metabolic shifts, improving predictive accuracy for systems biology research.

More Related Videos

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

4.2K
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

3.5K

Related Experiment Videos

Last Updated: Dec 21, 2025

Author Spotlight: Emerging Technologies and Advanced Tools for Decoding Metabolomics Data Analysis
07:11

Author Spotlight: Emerging Technologies and Advanced Tools for Decoding Metabolomics Data Analysis

Published on: November 10, 2023

3.1K
High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

4.2K
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

3.5K

Area of Science:

  • Systems Biology
  • Metabolic Engineering
  • Computational Biology

Background:

  • Flux Balance Analysis (FBA) is widely used for metabolic modeling.
  • Integrating gene expression data improves FBA model accuracy.
  • Current methods require subjective thresholding of expression data.

Purpose of the Study:

  • To develop a method for mapping gene expression data to metabolic models without arbitrary thresholds.
  • To create a functional metabolic model that accurately recapitulates expression dynamics.

Main Methods:

  • Metabolic Adjustment by Differential Expression (MADE) uses statistical significance of expression changes.
  • No arbitrary expression thresholds are required.
  • Implemented in Matlab with a mixed-integer linear program solver.

Main Results:

  • MADE accurately maps expression data to metabolic models.
  • The method successfully modeled metabolic adjustments in Saccharomyces cerevisiae during a shift in respiration.
  • Calculated gene states matched 98.7% of possible expression changes.

Conclusions:

  • MADE provides a robust method for integrating gene expression data into metabolic models.
  • The approach enhances the predictive accuracy of constraint-based metabolic models.
  • This facilitates a more precise understanding of metabolic regulation and adaptation.