CyLineUp: A Cytoscape app for visualizing data in network small multiples [version 1; peer review: 2 approved]

CyLineUp is a Cytoscape 3 app for the projection of high-throughput measurement data from multiple experiments/samples on a network or pathway map using "small multiples". This visualization method allows for easy comparison of different experiments in the context of the network or pathway...

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Bibliographic Details
Published inF1000 research Vol. 5; p. 635
Main Authors Costa, Maria Cecília D, Slijkhuis, Thijs, Ligterink, Wilco, Hilhorst, Henk W.M, de Ridder, Dick, Nijveen, Harm
Format Journal Article
LanguageEnglish
Published England Faculty of 1000 Ltd 2016
F1000Research
F1000 Research Ltd
Subjects
Bioinformatica
Bioinformatics
EPS
Laboratorium voor Plantenfysiologie
Laboratory of Plant Physiology
Plant Cell Biology
Software Tool
Expression profiling
Data display
Small multiples
Metabolite profiling
Graphical user interfaces
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Summary:CyLineUp is a Cytoscape 3 app for the projection of high-throughput measurement data from multiple experiments/samples on a network or pathway map using "small multiples". This visualization method allows for easy comparison of different experiments in the context of the network or pathway. The user can import various kinds of measurement data and select any appropriate Cytoscape network or WikiPathways pathway map. CyLineUp creates small multiples by replicating the loaded network as many times as there are experiments/samples (e.g. time points, stress conditions, tissues, etc.). The measurement data for each experiment are then mapped onto the nodes (genes, proteins etc.) of the corresponding network using a color gradient. Each step of creating the visualization can be customized to the user's needs. The results can be exported as a high quality vector image.
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The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
MCDC wrote the manuscript and provided experimental data to validate the use of the app. TS developed initial version of the app. WL, HWMH and DDR provided input on the manuscript. HN supervised app development, improved the app and provided input on the manuscript.
Competing interests: No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.8402.1