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

6.6K
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...
6.6K
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

12.7K
Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
12.7K
C4 Pathway and CAM01:27

C4 Pathway and CAM

46.6K
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...
46.6K
Protein Networks02:26

Protein Networks

4.1K
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,...
4.1K

You might also read

Related Articles

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

Sort by
Same author

Prediction of laser welding molten pool light intensity distribution based on an artificial neural network.

Science progress·2026
Same author

Hyaluronic acid-engineered infection-responsive liposomes achieve biofilm penetration and synergistic photothermal-photodynamic antibacterial therapy.

Carbohydrate polymers·2026
Same author

Linking changes in sulcal morphometry to cognitive development from childhood to adolescence.

Communications biology·2026
Same author

Spatiotemporal dynamics of the human cortical functional hierarchy across the lifespan.

Nature communications·2026
Same author

Correction: Photobiomodulation modulates mitochondrial energy metabolism and ameliorates neurological damage in an APP/PS1 mouse model of Alzheimer's disease.

Alzheimer's research & therapy·2026
Same author

Gut Microbiota-Targeted Photobiomodulation Ameliorates Alzheimer's Pathology via the Gut-Brain Axis: Comparable Efficacy to Transcranial Irradiation.

Microorganisms·2025
Same journal

Probabilistic RNA designability via interpretable ensemble approximation and dynamic decomposition.

Bioinformatics (Oxford, England)·2026
Same journal

Quantifying domain-specific relevance of computational biology Wikipedia articles using TF-IDF and cosine similarity.

Bioinformatics (Oxford, England)·2026
Same journal

GATSBI: improving context-aware protein embeddings through biologically motivated data splits.

Bioinformatics (Oxford, England)·2026
Same journal

BiMba: using Vision Mamba to predict protein sites that bind other proteins.

Bioinformatics (Oxford, England)·2026
Same journal

ProMeta: a meta-learning framework for robust disease diagnosis and prediction from plasma proteomics.

Bioinformatics (Oxford, England)·2026
Same journal

Is a Win-Win possible? Achieving pareto-optimal privacy-utility balance in fine-tuned genome language model embeddings against embedding reconstruction attacks.

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

Related Experiment Video

Updated: Oct 11, 2025

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

17.9K

SBGNview: towards data analysis, integration and visualization on all pathways.

Xiaoxi Dong1,2, Kovidh Vegesna1,2, Cory Brouwer1,2

  • 1Department of Bioinformatics and Genomics, College of Computing and Informatics, UNC Charlotte, Charlotte, NC 28223, USA.

Bioinformatics (Oxford, England)
|December 5, 2021
PubMed
Summary
This summary is machine-generated.

SBGNview is a new R package that enhances omics research by providing comprehensive pathway analysis and data visualization. It supports the Systems Biology Graphical Notation (SBGN) format, extending coverage to major pathway databases and offering advanced features over existing tools.

More Related Videos

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

3.4K
Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.3K

Related Experiment Videos

Last Updated: Oct 11, 2025

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

17.9K
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

3.4K
Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.3K

Area of Science:

  • Genomics and Omics Research
  • Bioinformatics
  • Systems Biology

Background:

  • Pathway analysis and data visualization are crucial in omics research.
  • Current tools have limitations in function, pathway coverage, and data format.

Purpose of the Study:

  • To develop SBGNview, a comprehensive R package for enhanced pathway analysis and data visualization.
  • To address limitations in existing tools regarding pathway coverage, data format, and functionality.

Main Methods:

  • Developed SBGNview, an R package adopting the Systems Biology Graphical Notation (SBGN) format.
  • Extended pathway coverage to major databases beyond KEGG, including over 5200 reference pathways and 3000 species.
  • Implemented features for high-quality SVG graphics, iterative editing, and interactive visualization (Highlighter module).

Main Results:

  • SBGNview significantly extends pathway coverage and visualization capabilities.
  • The package offers superior design and function compared to existing tools like Pathview.
  • Provides infrastructure for SBGN data manipulation and processing.

Conclusions:

  • SBGNview offers a comprehensive and flexible solution for pathway analysis and visualization in omics research.
  • The package enhances data interpretation and facilitates further updates through its interactive features.
  • SBGNview provides essential tools for working with SBGN data, advancing the field of systems biology.