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

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.