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Related Experiment Video

Updated: Mar 18, 2026

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

CyLineUp: A Cytoscape app for visualizing data in network small multiples.

Maria Cecília D Costa¹, Thijs Slijkhuis², Wilco Ligterink¹

¹Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.

|June 28, 2016

Summary

This summary is machine-generated.

CyLineUp is a Cytoscape 3 app that visualizes high-throughput measurement data across multiple experiments on biological networks. This tool enables easy comparison of experimental results within a network context.

Keywords:

Data display Expression profiling Graphical user interfaces Metabolite profiling Small multiples

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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
Systems Biology
Computational Biology

Background:

High-throughput measurement data requires effective visualization for biological network analysis.
Comparing data across multiple experiments (e.g., time points, conditions) on pathways is challenging.

Purpose of the Study:

To introduce CyLineUp, a Cytoscape 3 application for projecting and comparing high-throughput measurement data on network or pathway maps.
To provide a user-friendly tool for visualizing multi-experimental data in a network context.

Main Methods:

CyLineUp utilizes the 'small multiples' visualization technique, replicating networks for each experiment.
Users can import diverse measurement data and select Cytoscape networks or WikiPathways maps.
Measurement data is mapped onto network nodes (genes, proteins) using color gradients.

Main Results:

The application facilitates the direct comparison of experimental data across different conditions within a unified network view.
Customizable visualization parameters allow tailoring the output to specific research needs.
High-quality vector images of the visualizations can be exported for further analysis and publication.

Conclusions:

CyLineUp offers an effective solution for visualizing and comparing high-throughput data on biological networks.
The 'small multiples' approach enhances the interpretability of multi-experimental results in systems biology.
This tool supports researchers in understanding complex biological systems through integrated data visualization.