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This book comprises protocols describing systems biology methodologies and computational tools, offering a variety of ways to analyze different types of high-throughput cancer data. Chapters give an overview over data types available in large-scale data repositories and state-of-the-art methods used in the field of cancer systems biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Cancer Systems Biology : Methods and Protocols aims to ensure successful results in the further study of this vital field. The chapters "Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels", "Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research" and "Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells" are available open access under a CC BY 4.0 license via link.springer.com.