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Related Experiment Video

Updated: Dec 21, 2025

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

Visualize omics data on networks with Omics Visualizer, a Cytoscape App.

Marc Legeay¹, Nadezhda T Doncheva^1,2, John H Morris³

¹Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.

|July 15, 2020

Summary

This summary is machine-generated.

Omics Visualizer is a new Cytoscape app that visualizes complex omics data onto biological networks. It handles multiple data rows per node, enabling richer network analysis and visualization.

Keywords:

Cytoscape app network biology network visualization omics data

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Last Updated: Dec 21, 2025

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Published on: December 7, 2021

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Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore

Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore

Published on: December 12, 2019

Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Cytoscape is a widely used open-source platform for biological network analysis and visualization.
Standard Cytoscape data import is limited to one row of data per node.
Omics datasets frequently contain multiple entries per gene or protein, such as post-translational modifications or different conditions.

Purpose of the Study:

To introduce Omics Visualizer, a novel Cytoscape application designed to overcome limitations in visualizing complex omics data.
To enable the import and visualization of multi-row omics data tables onto biological networks.

Main Methods:

Omics Visualizer leverages the Cytoscape enhancedGraphics app for node-based visualizations.
Data is displayed using pie or donut charts within or around network nodes, with colors representing data values.
The app integrates with the Cytoscape stringApp to retrieve networks from the STRING database if none are provided.

Main Results:

Successfully developed and implemented Omics Visualizer app for Cytoscape.
Enabled visualization of multi-row omics data, including different modification sites, peptides, splice isoforms, or experimental conditions.
Facilitated integration with existing biological networks or retrieval from STRING.

Conclusions:

Omics Visualizer significantly enhances the capability of Cytoscape for analyzing and visualizing complex, multi-row omics data.
The app provides a flexible and powerful tool for researchers to explore omics datasets in the context of biological networks.
This facilitates deeper insights into biological processes and molecular interactions.