Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Vesicular Tubular Clusters

Vesicular Tubular Clusters

After budding out from the ER membrane, some COPII vesicles lose their coat and fuse with one another to form larger vesicles and interconnected tubules called vesicular tubular clusters or VTCs. These clusters constitute a compartment at the ER-Golgi interface known as ERGIC (Endoplasmic Reticulum Golgi Intermediate Compartment). The ERGIC is a mobile membrane-bound cargo transport system that sorts proteins secreted from ER and delivers them to the Golgi.
With the help of motor proteins such...

Molecular Models

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.

Intracellular Signaling Cascades

Intracellular Signaling Cascades

Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. The continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors, which cannot interact with most components of the cell, such as DNA. Only internal receptors can interact directly with DNA in the nucleus to initiate protein synthesis. When a ligand binds to its receptor, conformational changes occur that affect the...

Intracellular Signaling Cascades

Intracellular Signaling Cascades

Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. The continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors, which cannot interact with most components of the cell, such as DNA. Only internal receptors can interact directly with DNA in the nucleus to initiate protein synthesis. When a ligand binds to its receptor, conformational changes occur that affect the...

C4 Pathway and CAM

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...

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

You might also read

Related Articles

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

Sort by

Same author

VizCommender: Computing Text-Based Similarity in Visualization Repositories for Content-Based Recommendations.

IEEE transactions on visualization and computer graphics·2020

Same author

Oxido-reductive regulation of vascular remodeling by receptor tyrosine kinase ROS1.

The Journal of clinical investigation·2014

Same author

enhancedGraphics: a Cytoscape app for enhanced node graphics.

F1000Research·2014

Same author

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Nature biotechnology·2014

Same author

Mosaic: making biological sense of complex networks.

Bioinformatics (Oxford, England)·2012

Same author

GLay: community structure analysis of biological networks.

Bioinformatics (Oxford, England)·2010

Search research articles

Related Experiment Video

Updated: Jul 3, 2026

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

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

VistaClara: an expression browser plug-in for Cytoscape.

Robert Kincaid¹, Allan Kuchinsky, Michael Creech

¹Agilent Laboratories, Santa Clara, CA 95051, USA. robert_kincaid@agilent.com

Bioinformatics (Oxford, England)

|August 6, 2008

Summary

VistaClara offers enhanced gene and protein expression visualization within biological networks. This Cytoscape plug-in provides an interactive permutation matrix for flexible data exploration and analysis.

Related Experiment Videos

Last Updated: Jul 3, 2026

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

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

Area of Science:

Bioinformatics
Systems Biology
Computational Biology

Background:

Cytoscape is a widely used open-source software platform for visualizing complex biological networks.
Existing visualization methods in Cytoscape may lack flexibility for detailed gene and protein expression analysis.
There is a need for advanced tools to integrate and explore expression data within network contexts.

Purpose of the Study:

To introduce VistaClara, a novel plug-in for Cytoscape.
To provide a more flexible and interactive method for visualizing gene and protein expression data.
To enhance the analytical capabilities of Cytoscape for systems biology research.

Main Methods:

Development of VistaClara as a plug-in for the Cytoscape platform.
Implementation of an extended attribute browser using a graphical and interactive permutation matrix.
Design of the permutation matrix to resemble heat map displays common in gene-expression analysis.

Main Results:

VistaClara enables flexible visualization of gene and protein expression within network contexts.
The interactive permutation matrix offers advanced display options and user interactions.
The tool facilitates a deeper exploration of expression patterns in relation to biological networks.

Conclusions:

VistaClara significantly enhances the visualization and analysis of gene and protein expression data in Cytoscape.
The plug-in provides novel functionalities not previously available, improving network-based expression studies.
VistaClara represents a valuable tool for researchers in bioinformatics and systems biology.