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

Cardiovascular risks and hazards associated with deep space exploration.

Communications medicine·2026
Same author

Transcriptomic profiling identifies immunotherapy-responsive phenotypes in microsatellite-stable metastatic colorectal cancer.

Oncogene·2026
Same author

Endothelial dysfunction and metabolic biomarkers in post-COVID-19 syndrome.

Scientific reports·2026
Same author

Spotting a unicorn: spatial transcriptome analysis of the eyelid reveals gene regulatory networks enriched in Moll glands.

Briefings in bioinformatics·2026
Same author

Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma.

Nature cancer·2026
Same author

Growth Differentiation Factor 15 (GDF-15) as a modulator of hepatic steatosis and fibrosis: insights from a 6-year retrospective cohort study.

Frontiers in medicine·2026
Same journal

Association between intestinal functional disorders and anal fistula: evidence from a retrospective case-control study.

PeerJ·2026
Same journal

Automated recognition of Meso-Cenozoic foraminifera from Senegalese sedimentary deposits using convolutional neural networks.

PeerJ·2026
Same journal

Genome-wide analysis of <i>HSP70</i> gene superfamily in kelp (<i>Saccharina japonica</i>): identification, characterization, and heat stress-responsive expression profiles.

PeerJ·2026
Same journal

Morphological and molecular evidence of the Antarctic sleeper shark <i>Somniosus antarcticus</i> (Somniosidae) in northern Chile.

PeerJ·2026
Same journal

Stroboscopic balance training enhances dynamic stability and postural control in collegiate badminton players: a randomized controlled trial.

PeerJ·2026
Same journal

Frequent exposure to biologics is associated with small intestinal bacterial overgrowth in patients with Crohn's disease: a retrospective case-control study.

PeerJ·2026
See all related articles

Related Experiment Video

Updated: Sep 11, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

5.0K

Topology-aware pathway analysis of spatial transcriptomics.

Siras Hakobyan1, Maria Schmidt2, Hans Binder2,3

  • 1Bioinformatics Group, Institute of Molecular Biology NAS RA, Yerevan, Armenia.

Peerj
|August 19, 2025
PubMed
Summary
This summary is machine-generated.

Pathway Signal Flow (PSF) algorithm translates gene expression into pathway activity, revealing spatial signaling events. This method enhances spatial transcriptomics analysis by capturing pathway topology and intercellular communication.

Keywords:
10x VisiumCancer omicsCell–cell interactionFunctional analysisMelanomaSignaling pathwaysSpatial transcriptomicsTopology-aware pathway analysisTumour microenvironmentVisualization

More Related Videos

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics
07:43

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

3.2K
Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System
08:54

Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System

Published on: March 20, 2016

9.9K

Related Experiment Videos

Last Updated: Sep 11, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

5.0K
Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics
07:43

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

3.2K
Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System
08:54

Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System

Published on: March 20, 2016

9.9K

Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology
  • Spatial Transcriptomics

Background:

  • Spatial transcriptomics (ST) maps gene expression to tissue architecture, revealing cellular interactions missed by other methods.
  • Traditional ST analysis often overlooks pathway connectivity and topology, limiting the understanding of signaling propagation.
  • Existing spatially-aware methods primarily focus on individual genes, potentially missing broader pathway dynamics.

Purpose of the Study:

  • To introduce the Pathway Signal Flow (PSF) algorithm for translating gene expression into pathway-level activity.
  • To assess PSF's ability to capture pathway topology and identify spatially deregulated signaling events.
  • To compare PSF with existing ST analysis methods for clustering and functional annotation.

Main Methods:

  • Developed the Pathway Signal Flow (PSF) algorithm to integrate gene expression with interaction networks, calculating branch-specific pathway activity scores.
  • Applied PSF to human melanoma and mouse brain 10x Visium datasets, analyzing 40 Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways.
  • Compared PSF-based clustering with standard Seurat Louvain, Vesalius, and spatialGE; compared functional annotation with overrepresentation analysis (ORA) and GSDensity.

Main Results:

  • PSF-based clustering showed good correspondence with expression-based clustering when using spatially aware methods.
  • PSF identified a broader set of significant pathways than ORA and GSDensity, demonstrating increased sensitivity due to branch-level resolution.
  • PSF successfully detected spatially deregulated pathway branches and identified potential intercellular communication via ligand-receptor interactions.

Conclusions:

  • PSF effectively translates gene expression into branch-level pathway activities, enhancing spatial transcriptomics analysis.
  • The algorithm provides a functionally annotated feature space capturing downstream signaling effects and pathway topology.
  • PSF offers a sensitive and comprehensive approach for identifying spatially deregulated processes and intercellular communication in tissues.