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

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...
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

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 produces two-second...
Three-Dimensional Microscopy in Microbiology01:28

Three-Dimensional Microscopy in Microbiology

Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Protein Networks02:26

Protein Networks

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,...
Protein Networks02:26

Protein Networks

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,...

You might also read

Related Articles

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

Sort by
Same author

Adjunctive intra-arterial alteplase after near-complete or complete reperfusion in acute ischemic stroke: A post hoc analysis of the PEARL Trial.

International journal of stroke : official journal of the International Stroke Society·2026
Same author

KEGG Syntax for comparison of organisms, organism groups, and viruses by conserved gene repertoires.

Protein science : a publication of the Protein Society·2026
Same author

Identification of Two Novel Variants in <i>CRYGD</i> and <i>OCRL</i> Genes in the Chinese Population With Hereditary Congenital Cataracts Using Whole Exome Sequencing.

Human mutation·2026
Same author

Prenatal diagnosis and molecular cytogenetic analysis of Xp22.31 microdeletions and microduplications in Chinese populations.

BMC pregnancy and childbirth·2026
Same author

Targeting HIF-1α rescues microglial efferocytosis via the SLC7A11-TAM pathway to ameliorate Sepsis-associated encephalopathy.

International immunopharmacology·2026
Same author

Accurate SPARQL generation via in-context learning and schema-based query construction.

Bioinformatics (Oxford, England)·2026

Related Experiment Video

Updated: Jul 14, 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

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

Zhenjun Hu1, David M Ng, Takuji Yamada

  • 1Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA.

Nucleic Acids Research
|June 26, 2007
PubMed
Summary

VisANT 3.0 integrates pathway databases and expression data for exploratory pathway analysis. This tool aids in visualizing, annotating, and inferring gene pathways, enhancing biological discovery.

More Related Videos

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo
08:32

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo

Published on: May 4, 2018

New Features in Visual Dynamics 3.0
05:00

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Related Experiment Videos

Last Updated: Jul 14, 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

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo
08:32

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo

Published on: May 4, 2018

New Features in Visual Dynamics 3.0
05:00

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Pathway analysis is crucial for understanding biological processes.
  • Existing tools often lack integrated visualization and data analysis capabilities.
  • The KEGG and Predictome databases offer valuable pathway information.

Purpose of the Study:

  • To introduce VisANT 3.0, an enhanced platform for exploratory pathway analysis.
  • To enable multi-scale visualization and annotation of biological pathways.
  • To facilitate the inference of gene/protein functions and pathways using expression data.

Main Methods:

  • Integration of KEGG and Predictome databases with coexpression analysis tools.
  • Utilized data from Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO).
  • Developed multi-scale visualization, editing, and annotation features compatible with KEGG notation.

Main Results:

  • VisANT 3.0 supports visualization of expression data within pathway contexts.
  • Enrichment of known KEGG pathways and inference of novel pathways are possible.
  • Pathways can be exported in various formats including VisML, images, and SVG.

Conclusions:

  • VisANT 3.0 provides a comprehensive platform for pathway exploration and analysis.
  • The tool facilitates the discovery of gene functions and biological pathways.
  • VisML format allows for secure sharing and online publication of pathways.