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

Protein Networks02:26

Protein Networks

3.7K
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,...
3.7K
Protein Networks02:26

Protein Networks

1.8K
1.8K
Genomics02:02

Genomics

35.5K
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...
35.5K
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

4.7K
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...
4.7K
Proteomics01:33

Proteomics

7.5K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
7.5K

You might also read

Related Articles

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

Sort by
Same author

The Era of Large-Scale Data in Biological Sciences.

Advances in experimental medicine and biology·2026
Same author

Interactomics: Dissecting Protein Networks in Living Systems.

Advances in experimental medicine and biology·2026
Same author

Primer on Modelling Approaches for Omics Data.

Advances in experimental medicine and biology·2026
Same author

When neighbors play a role: A systems-level analysis of protein interactions conditioning cancer driver mutation effects.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Tonic signaling of the B-cell antigen-specific receptor is a common functional hallmark in chronic lymphocytic leukemia cell phosphoproteomes at early disease stages.

Molecular oncology·2025
Same author

Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation.

International journal of molecular sciences·2024

Related Experiment Video

Updated: May 5, 2026

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 Interpretation of Omics Data: From Pathways to Networks.

Marina L García-Vaquero1, João A I Miranda1, Margarida Carrolo2

  • 1BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal.

Advances in Experimental Medicine and Biology
|May 3, 2026
PubMed
Summary
This summary is machine-generated.

This study explains computational methods for interpreting omics data, focusing on Over-Representation Analysis (ORA) and Functional Class Scoring (FCS). It also covers network biology approaches like Centrality Analysis for enhanced functional interpretation of molecular ensembles.

Keywords:
Biological networksFunctional Class ScoringNetwork centralityNetwork clusteringNetwork diffusionOver-Representation Analysis

More Related Videos

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

2.7K
A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

2.6K

Related Experiment Videos

Last Updated: May 5, 2026

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
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

2.7K
A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

2.6K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Omics experiments generate lists of molecular entities requiring functional interpretation.
  • Interpreting these molecules as functionally related ensembles is crucial for biological insight.
  • Existing computational methods aim to identify relevant functions and pathways within omics data.

Purpose of the Study:

  • To describe the principles behind computational methods for functional interpretation of omics data.
  • To discuss the application of these methods in understanding molecular ensembles.
  • To provide an overview of Over-Representation Analysis (ORA), Functional Class Scoring (FCS), and network analysis techniques.

Main Methods:

  • Explanation of Over-Representation Analysis (ORA) for identifying enriched functional annotations.
  • Description of Functional Class Scoring (FCS) for assessing pathway relevance.
  • Introduction to network biology concepts and analysis methods (Centrality Analysis, Network Clustering, Network diffusion).

Main Results:

  • ORA and FCS are presented as primary approaches for functional annotation of biomolecule lists.
  • Network analysis methods are introduced as tools to enhance the functional interpretation of omics data.
  • The chapter outlines how different computational strategies can be combined for comprehensive analysis.

Conclusions:

  • Computational methods are essential for interpreting complex omics datasets.
  • Both statistical enrichment analyses (ORA, FCS) and network-based approaches are valuable for functional interpretation.
  • Integrating diverse computational strategies potentiates deeper biological insights from omics data.