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

Diversity in Cell Signaling Responses01:22

Diversity in Cell Signaling Responses

The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity. 
Graded and Abrupt Responses
Some signaling systems generate...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
Interactions Between Signaling Pathways01:19

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...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

You might also read

Related Articles

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

Sort by
Same author

Coronary Artery Calcium Scans by Area Deprivation Index in a Multicenter Health System.

JACC. Advances·2026
Same author

Cohort Study of Initial Diuretic Dosing and Outcomes Among Patients Hospitalized for Congestive Heart Failure: Insights From the Cardiovascular Quality Improvement and Care Innovation Consortium.

Journal of the American Heart Association·2026
Same author

Association Between Artificial Intelligence-Detected Features on the ECG and Presence of Microvascular Obstruction.

Circulation. Cardiovascular interventions·2025
Same author

Three-Year Outcomes of Second Bioprosthesis After Early Surgical Aortic Bioprosthetic Failure.

JACC. Advances·2025
Same author

High-Profile Cardiac Arrests Correlate With Online Searches and Public Interest: A Call for Action.

Journal of the American Heart Association·2025
Same author

Incidence, predictors and outcomes of tricuspid regurgitation progression after left-sided valvular intervention.

Heart (British Cardiac Society)·2025
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026
Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026
Same journal

CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment.

PLoS computational biology·2026
Same journal

Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.

PLoS computational biology·2026
Same journal

Neuronal excitability and parameter variability in the Hodgkin-Huxley model.

PLoS computational biology·2026
See all related articles

Related Experiment Video

Updated: May 13, 2026

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

Differential expression analysis for pathways.

Winston A Haynes1, Roger Higdon, Larissa Stanberry

  • 1Bioinformatics & High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington, USA.

Plos Computational Biology
|March 22, 2013
PubMed
Summary
This summary is machine-generated.

Differential Expression Analysis for Pathways (DEAP) improves biological pathway analysis by integrating pathway structure. DEAP significantly enhances the detection of regulatory patterns in gene and protein expression data.

More Related Videos

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

Related Experiment Videos

Last Updated: May 13, 2026

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

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • Life science research generates vast amounts of data crucial for understanding biological functions and diseases.
  • Existing methods for analyzing differential expression data often overlook valuable pathway information.

Purpose of the Study:

  • To introduce DEAP (Differential Expression Analysis for Pathways), a novel approach for identifying regulatory patterns.
  • To leverage biological pathway information, including structure, to improve differential expression analysis.

Main Methods:

  • DEAP integrates pathway structure into differential expression analysis.
  • It identifies the most differentially expressed segments within biological pathways.
  • Performance was evaluated on simulated data and real-world gene and protein expression studies.

Main Results:

  • DEAP significantly outperformed traditional methods on simulated data, increasing power by up to two orders of magnitude.
  • It identified fourteen important pathways missed by existing methods in studies of chronic obstructive pulmonary disease and interferon treatment.
  • In an interferon study, DEAP pinpointed a critical four-protein pathway within the Notch signaling pathway.

Conclusions:

  • DEAP offers a substantial improvement over existing methods for analyzing differential expression data.
  • The approach enhances the discovery of biologically relevant pathways and regulatory patterns.
  • DEAP provides a more focused and powerful tool for interpreting complex biological data.