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

Phylogeny

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

Phylogenetic Trees

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

pV-Diagrams

pV-Diagrams

The pV diagram, which is a graph of pressure versus volume of the gas under study, is helpful in describing certain aspects of the substance. When the substance behaves like an ideal gas, the ideal gas equation describes the relationship between its pressure and volume. On a pV diagram, it is common to plot an isotherm, which is a curve showing p as a function of V with the number of molecules and the temperature fixed. Then, for an ideal gas, the product of the pressure of the gas and its...

Modified Boxplots

Modified Boxplots

A standard box and whisker plot informs us about the spread of the data in a given sample. One can identify the minimum value, maximum value, first quartile value, second quartile or median value, and third quartile.
However, the box plot does not tell the reader about outliers - values that lie far from the center of the data. We can modify the standard box and whisker plot to identify the outliers and visualize the actual spread of the data in a sample.
Initially, we calculate the adjusted...

Karyotyping

Karyotyping

You might also read

Related Articles

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

Sort by

Same author

Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.

Molecular biology of the cell·2005

Same author

Gene expression diversity among Mycobacterium tuberculosis clinical isolates.

Microbiology (Reading, England)·2005

Same author

Nutritional homeostasis in batch and steady-state culture of yeast.

Molecular biology of the cell·2004

Same author

Identification and functional analysis of human transcriptional promoters.

Genome research·2003

Same author

Identification of genes periodically expressed in the human cell cycle and their expression in tumors.

Molecular biology of the cell·2002

Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026

Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026

Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026

Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026

Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026

Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 2, 2026

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

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

Published on: December 7, 2021

Java Treeview--extensible visualization of microarray data.

Alok J Saldanha¹

¹Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. alokito@users.sourceforge.net

Bioinformatics (Oxford, England)

|June 8, 2004

Summary

This summary is machine-generated.

Java Treeview offers an open-source, cross-platform solution for visualizing large microarray datasets. This enhanced software encourages innovation and extends functionality, making complex data analysis more accessible.

More Related Videos

A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development

A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development

Published on: October 29, 2019

Rapid High-throughput Species Identification of Botanical Material Using Direct Analysis in Real Time High Resolution Mass Spectrometry

Rapid High-throughput Species Identification of Botanical Material Using Direct Analysis in Real Time High Resolution Mass Spectrometry

Published on: October 2, 2016

Related Experiment Videos

Last Updated: Jan 2, 2026

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

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

Published on: December 7, 2021

A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development

A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development

Published on: October 29, 2019

Rapid High-throughput Species Identification of Botanical Material Using Direct Analysis in Real Time High Resolution Mass Spectrometry

Rapid High-throughput Species Identification of Botanical Material Using Direct Analysis in Real Time High Resolution Mass Spectrometry

Published on: October 2, 2016

Area of Science:

Bioinformatics
Computational Biology
Data Visualization

Background:

Existing microarray visualization tools like Treeview are often closed-source and platform-specific.
This limits their utility, extensibility, and suitability for broader research applications.
Innovation in data analysis is hindered by restricted access to visualization software.

Purpose of the Study:

To introduce Java Treeview as an open-source, cross-platform alternative for microarray data visualization.
To highlight its capability in handling large datasets and supporting file format extensions.
To promote Java Treeview as a versatile platform for comparative analysis and visualization.

Main Methods:

Development of Java Treeview as a rewrite of the original Treeview application.
Implementation of open-source principles to allow user modification and extension.
Support for extensible file formats to integrate results from additional analyses.
Creation of an applet version for easy web-based deployment.

Main Results:

Java Treeview successfully handles very large microarray datasets.
The software supports extensions to its file format, enabling visualization of comparative analysis results.
An applet version allows for seamless integration into any website without server-side configuration.
The open-source nature fosters innovation and broader adoption in the scientific community.

Conclusions:

Java Treeview provides a powerful, flexible, and accessible solution for microarray data visualization.
Its open-source and cross-platform design overcomes limitations of previous tools.
It serves as an attractive platform for researchers needing to visualize and compare complex biological data.