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

7.2K
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...
7.2K
Genomics02:02

Genomics

39.6K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
39.6K
Synthetic Biology02:55

Synthetic Biology

5.5K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
5.5K
C4 Pathway and CAM01:27

C4 Pathway and CAM

48.7K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
48.7K

You might also read

Related Articles

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

Sort by
Same author

Rocuronium Dose and First-Attempt Intubation Success in the Critically Ill: Secondary Analysis of Two Multicenter Trials.

American journal of respiratory and critical care medicine·2026
Same author

A Head and Neck Cancer Patient-Specific Microphysiological System for Predicting Response to Chemoradiation.

bioRxiv : the preprint server for biology·2026
Same author

Genetic complementation reveals structure-function links in nodavirus RNA replication complex crowns.

PLoS pathogens·2026
Same author

United Global Advocacy Drives Updates to World Health Organization Essential Medicines List.

Haemophilia : the official journal of the World Federation of Hemophilia·2026
Same author

Integrated Multi-omic Profiling Identifies BRD8/EP400 as a Pivotal Chromatin Module Mediating Anti-HER2 Response in HR+/HER2+ Breast Cancer.

Cancer research·2026
Same author

Impact of measurable residual disease on outcomes using a modified DFCI protocol for adults with BCR-ABL negative acute lymphoblastic leukemia.

Leukemia research·2026
Same journal

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

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

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

Related Experiment Video

Updated: Jan 16, 2026

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

18.4K

MPAC: a computational framework for inferring pathway activities from multi-omic data.

Peng Liu1,2, David Page1,2,3, Paul Ahlquist4,5,6

  • 1Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, United States.

Bioinformatics (Oxford, England)
|October 4, 2025
PubMed
Summary
This summary is machine-generated.

We developed Multi-omic Pathway Analysis of Cells (MPAC), a computational framework for analyzing complex multi-omic data. MPAC identifies patient subgroups and key proteins linked to clinical outcomes, improving disease analysis.

More Related Videos

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

900
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

3.7K

Related Experiment Videos

Last Updated: Jan 16, 2026

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

18.4K
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

900
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

3.7K

Area of Science:

  • Computational biology
  • Bioinformatics
  • Systems biology

Background:

  • Accurate cellular state assessment requires integrating multi-omic data (genomic, epigenomic, transcriptomic, proteomic).
  • Computational modeling of multi-omic data aids disease analysis by revealing patient subgroups and informing clinical outcomes.

Purpose of the Study:

  • To present Multi-omic Pathway Analysis of Cells (MPAC), a framework for interpreting multi-omic data using biological pathway knowledge.
  • To demonstrate MPAC's ability to infer consensus protein activity levels and group samples by pathway activities for clinical relevance.

Main Methods:

  • MPAC utilizes factor graphs to encode network relationships from biological pathways.
  • It infers consensus activity levels for proteins and pathway entities from multi-omic data.
  • Permutation testing is employed to eliminate spurious activity predictions, and samples are grouped by pathway activities.

Main Results:

  • MPAC identified a patient subgroup related to immune responses in head and neck squamous cell carcinoma, which was not detected by analyzing individual omic data types.
  • Key proteins within this subgroup showed pathway activities associated with clinical outcomes and immune cell composition.
  • The MPAC R package facilitates similar multi-omic analyses on new datasets.

Conclusions:

  • MPAC provides a robust computational framework for multi-omic data analysis.
  • The framework can uncover novel patient subgroups and identify clinically relevant proteins.
  • MPAC enhances the understanding of complex diseases by integrating diverse biological data.