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

C4 Pathway and CAM01:27

C4 Pathway and CAM

37.9K
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...
37.9K
Studying the Cytoskeleton01:17

Studying the Cytoskeleton

8.2K
The cytoskeletal architecture can be studied using different microscopic and biochemical techniques. Electron microscopy was instrumental in discovering the cytoskeletal architecture around the 1960s, which allowed obtaining structural information at a high-resolution level. However, the sample preparation procedure often limits this ability in biological samples. Several protocols have been developed over the years to optimize sample preparation. In one of the protocols known as rotary...
8.2K
cAMP-dependent Protein Kinase Pathways01:25

cAMP-dependent Protein Kinase Pathways

7.2K
Cyclic Adenosine Monophosphate (cAMP) is an essential second messenger that activates protein kinase A (PKA) and regulates various biological processes. A single epinephrine molecule binds to GPCR and activates several heterotrimeric G proteins, each stimulating multiple adenylyl cyclase, amplifying the signal, and synthesizing large numbers of cAMP molecules. Small changes in cAMP concentration affect PKA activity. The binding of four cAMP molecules induces a conformational change in PKA,...
7.2K
Cytoskeletal Coordination in Cell Migration01:32

Cytoskeletal Coordination in Cell Migration

4.8K
A migrating cell changes its shape during the cyclic events of attachment and detachment from the substratum and repositions the cell organelles correspondingly. These complex events are orchestrated by the dynamic cytoskeletal network comprising actin filaments, intermediate filaments, and microtubules. Cytoskeletal crosstalk — the direct and indirect communication between the different components — is crucial for this coordination. Direct communication involves various linker...
4.8K
Flow Cytometry01:23

Flow Cytometry

13.1K
The development of flow cytometry techniques began in 1934 with initial attempts by Andrew Moldavan, a bacteriologist who counted the cells in a flowing capillary system. Moldavan pumped cells through a capillary tube focused under a microscope for visualization. The invention of photometry allowed the measurement of differentially-stained cells, and Louis Kamentsky developed the first multiparameter flow cytometer in 1965 to identify and count the cancer cells in cervical tissue specimens.
In...
13.1K
Synthetic Biology02:55

Synthetic Biology

4.4K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
4.4K

You might also read

Related Articles

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

Sort by
Same author

Final analysis of phase 2 clinical trial of ruxolitinib and azacitidine combination therapy in patients with myelodysplastic syndrome/myeloproliferative neoplasms.

Journal of hematology & oncology·2026
Same author

All-Oral Combination of Revumenib, Decitabine, and Venetoclax for Relapsed or Refractory AML (SAVE).

Journal of clinical oncology : official journal of the American Society of Clinical Oncology·2026
Same author

Prognostic impact of ASXL1 mutations in acute myeloid leukemia treated with lower intensity therapy.

Cancer·2026
Same author

BB-EIT: A Generalized Prediction Model for Protein Adsorption on Polymer Brushes Using Augmented Chemical Embeddings.

ACS applied materials & interfaces·2026
Same author

Clonal dynamics of CH in CLL.

Blood·2026
Same author

Immunophenotypic changes following menin inhibition in acute myeloid leukemia.

Leukemia·2026
Same journal

Exploring potential strategies to enhance memory and cognition in aging mice.

F1000Research·2026
Same journal

Construction an Implicit Block Multi-Steps Approach for Solving Sixth-Order Fractional Differential Equations.

F1000Research·2026
Same journal

Kansei Engineering in the Evolving Service Sector: A Decade of Insights.

F1000Research·2026
Same journal

A Safety-First Mindset:  Role of Patient Safety Culture in Enhancing Healthcare Workers' Emotional Intelligence.

F1000Research·2026
Same journal

Decoding Decisions: Personality-Interest Motivational Sequences as Predictors of Career Paths.

F1000Research·2026
Same journal

Beyond the Transparent Barrier: A Domain Visualization and Integrative Review of Contemporary Research on Gender-Based Professional Stasis.

F1000Research·2026
See all related articles

Related Experiment Video

Updated: Apr 24, 2026

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

21.2K

KEGGscape: a Cytoscape app for pathway data integration.

Kozo Nishida1, Keiichiro Ono2, Shigehiko Kanaya3

  • 1Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, 565-0874, Japan ; JST, National Bioscience Database Center (NBDC), Tokyo, 102-0081, Japan.

F1000Research
|September 2, 2014
PubMed
Summary
This summary is machine-generated.

KEGGscape integrates KEGG pathway data into Cytoscape for detailed visualization and analysis. This tool enables complex, interactive biological system representations beyond the KEGG PATHWAY web application.

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

4.7K
ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
05:12

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

11.2K

Related Experiment Videos

Last Updated: Apr 24, 2026

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

21.2K
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

4.7K
ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
05:12

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

11.2K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • KEGG is a vital resource for curated biological pathways.
  • Existing tools may limit the complexity and interactivity of pathway visualizations.
  • Cytoscape offers a robust platform for biological network visualization and analysis.

Purpose of the Study:

  • Introduce KEGGscape, a Cytoscape application for integrating and visualizing KEGG pathway data.
  • Enable users to reproduce KEGG pathway diagrams within Cytoscape with high fidelity.
  • Facilitate advanced pathway analysis and the creation of interactive visualizations.

Main Methods:

  • KEGGscape leverages the KEGG database to import pathway information.
  • It utilizes Cytoscape's core visualization engine (Visual Style) for diagram rendering.
  • The app supports integration with other Cytoscape applications for pathway analysis.

Main Results:

  • KEGGscape successfully reproduces KEGG pathways in Cytoscape with detailed accuracy.
  • Users can import and visualize pathway datasets, creating biologist-friendly diagrams.
  • Complex, interactive visualizations integrating experimental data were generated.

Conclusions:

  • KEGGscape enhances biological systems visualization by combining KEGG data with Cytoscape's capabilities.
  • It offers advanced interactive visualization and analysis features not available in the KEGG PATHWAY web application.
  • The tool facilitates a deeper understanding of biological systems through integrated pathway and experimental data visualization.