Titlebook: Cancer Systems Biology; Methods and Protocol Louise von Stechow Book 2018 Springer Science+Business Media LLC 2018 somatic mutational netwo

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Quantitative Analysis of Tyrosine Kinase Signaling Across Differentially Embedded Human Glioblastomased to identify tyrosine kinase signaling networks present in these tumors and reveal the differential expression of functionally related proteins. This chapter provides the quantitative mass spectrometry methods required for the identification of in vivo oncogenic signaling networks from human tumor specimens.

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Profiling Tumor Infiltrating Immune Cells with CIBERSORTrom purified leukocyte subsets, CIBERSORT can accurately estimate the immune composition of a tumor biopsy. In this chapter, we provide a primer on the CIBERSORT method and illustrate its use for characterizing TILs in tumor samples profiled by microarray or RNA-Seq.

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Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panelsreens to identify genetic dependencies associated with particular molecular features. We describe the steps required to process the siRNA screen data, integrate the results with genotypic information to identify genetic dependencies, and finally the integration of protein-protein interaction data to interpret these dependencies.

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Book 2018 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 introductio

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Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Researchl computational tools and methods. In this chapter, we provide a detailed description of standard analysis steps for a clinical proteomics dataset performed in Perseus, a software for functional analysis of large-scale quantitative omics data.

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