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Related Concept Videos

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,...
pV-Diagrams01:18

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...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Related Experiment Video

Updated: Jun 22, 2026

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

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.

Zhenjun Hu1, Jui-Hung Hung, Yan Wang

  • 1Center for Advanced Genomic Technology, Program in Bioinformatics, Boston University, Boston, MA 02215, USA. zhenjun.hu@gmail.com

Nucleic Acids Research
|May 26, 2009
PubMed
Summary

VisANT software now integrates Gene Ontology (GO) for enhanced biological network analysis, enabling visualization, flexible annotation, and identification of enriched GO terms within networks.

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Last Updated: Jun 22, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Gene Ontology (GO) is widely used for functional annotation but often overlooks network correlations.
  • Existing network analysis tools have limitations in integrating GO hierarchies and network topology.

Purpose of the Study:

  • To introduce new capabilities in VisANT for advanced Gene Ontology (GO) integration in biological network analysis.
  • To extend the application of GO beyond simple functional annotation to network visualization, analysis, and inference.

Main Methods:

  • Developed a tree-based browser for visualizing GO hierarchies and integrating them with biological networks.
  • Implemented flexible annotation schemas allowing gene annotation at various abstraction levels.
  • Introduced algorithms for detecting over-represented GO terms in sub-networks and enriched GO modules in datasets, considering network topology.

Main Results:

  • VisANT now supports multi-scale visualization and analysis by integrating GO hierarchies with network structures.
  • Users can annotate genes at customized levels of detail, enhancing functional interpretation.
  • New algorithms effectively identify GO term enrichment and expression-enriched GO modules, incorporating network correlations.

Conclusions:

  • VisANT's enhanced capabilities significantly improve the utility of Gene Ontology in biological network analysis.
  • The software facilitates deeper insights into gene function and biological pathways by integrating ontological and network information.
  • VisANT provides a powerful, freely available platform for advanced network-based biological research.