Abstract
Cytoscape is an open-source software for visualizing, analyzing, and modeling biological networks. This chapter explains how to use Cytoscape to analyze the functional effect of sequence variations in the context of biological networks such as protein–protein interaction networks and signaling pathways. The chapter is divided into five parts: (1) obtaining information about the functional effect of sequence variation in a Cytoscape readable format, (2) loading and displaying different types of biological networks in Cytoscape, (3) integrating the genomic information (SNPs and mutations) with the biological networks, and (4) analyzing the effect of the genomic perturbation onto the network structure using Cytoscape built-in functions. Finally, we briefly outline how the integrated data can help in building mathematical network models for analyzing the effect of the sequence variation onto the dynamics of the biological system. Each part is illustrated by step-by-step instructions on an example use case and visualized by many screenshots and figures.
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Acknowledgements
This tutorial was inspired by the study of integrating information about sequence variations with biological networks published in 2009 [9]. First of all, I want to thank Laura I. Furlong who designed that study and who helped in developing a similar tutorial. I also want to thank Ferran Sanz for helpful discussions and Frank Wallrapp for reading the manuscript and testing the tutorial. Moreover, I want to thank Nicolas Le Novère who invited me to teach this tutorial in the EMBO/FEBS course and especially Vicky Schneider who invited me to write this chapter.
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Bauer-Mehren, A. (2013). Integration of Genomic Information with Biological Networks Using Cytoscape. In: Schneider, M. (eds) In Silico Systems Biology. Methods in Molecular Biology, vol 1021. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-450-0_3
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DOI: https://doi.org/10.1007/978-1-62703-450-0_3
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