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

You might also read

Related Articles

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

Sort by
Same author

Staphylococcal proliferation on skin models to investigate novel anti-infective treatments against dysbiosis.

Bioengineering & translational medicine·2026
Same author

HERA: a web server for host element reference-based aligner.

Nucleic acids research·2026
Same author

RegRegSEA: a web server for regulatory region set enrichment analysis of epigenomic data.

Nucleic acids research·2026
Same author

Probiotic Lactobacillus rhamnosus mitigates PBC-like features in Mcpip1-deficient mice via modulation of gut-liver crosstalk.

Biochimica et biophysica acta. Molecular basis of disease·2026
Same author

Benchmarking large language models for pathogen-disease classification in post-acute infection syndromes.

Briefings in bioinformatics·2026
Same author

mRNA Sequencing of Limbal Epithelial Cells and mRNA/miRNA Profiling of Limbal Stromal Cells in <i>PAX6</i>-Related Congenital Aniridia.

Cells·2026
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

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

Related Experiment Video

Updated: Jun 20, 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

A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.

Andreas Keller1, Christina Backes, Andreas Gerasch

  • 1Center for Bioinformatics, Saarland University, Building E.1.1, Saarbrücken, Germany. ack@bioinf.uni-sb.de

Bioinformatics (Oxford, England)
|August 29, 2009
PubMed
Summary
This summary is machine-generated.

We developed FiDePa, a new algorithm to find deregulated signaling pathways in tumors by analyzing gene expression. This method aids in identifying tumor-specific features for better cancer therapy.

More Related Videos

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
09:35

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research

Published on: August 16, 2017

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: Jun 20, 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

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
09:35

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research

Published on: August 16, 2017

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
  • Computational Biology
  • Systems Biology

Background:

  • Deregulated signaling cascades are critical in tumor initiation and progression.
  • High-throughput gene expression profiling enables detailed study of signaling networks.

Purpose of the Study:

  • To introduce a novel dynamic programming algorithm, FiDePa (Finding Deregulated Paths), for detecting deregulated signaling cascades.
  • To enable the identification of tumor-specific regulatory features for optimizing cancer therapy.

Main Methods:

  • Developed the FiDePa algorithm using dynamic programming.
  • Interpreted gene expression differences between tumor and normal tissues.
  • Utilized gene set enrichment analysis (GSEA) to identify enriched paths in regulatory networks.

Main Results:

  • FiDePa efficiently detects significantly enriched paths of differentially expressed genes/proteins.
  • Analysis of a glioma dataset revealed known key genes and pathways in cancer.
  • Correlated detected paths with clinical features such as necrosis and metastasis.

Conclusions:

  • FiDePa is a powerful tool for identifying deregulated signaling pathways in cancer.
  • The algorithm facilitates the discovery of tumor-specific targets for therapeutic intervention.
  • The approach aids in understanding the molecular basis of cancer progression and heterogeneity.