Cancer Systems Biology: Methods and Protocols

Description

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. Front Matter ....Pages i-xi Front Matter ....Pages 1-1 Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity Analysis (Hua Tan, Xiaobo Zhou)....Pages 3-11 Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data (Amanda J. Kedaigle, Ernest Fraenkel)....Pages 13-26 Analyzing DNA Methylation Patterns During Tumor Evolution (Heng Pan, Olivier Elemento)....Pages 27-53 MicroRNA Networks in Breast Cancer Cells (Andliena Tahiri, Miriam R. Aure, Vessela N. Kristensen)....Pages 55-81 Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels (James Campbell, Colm J. Ryan, Christopher J. Lord)....Pages 83-99 Front Matter ....Pages 101-101 Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells (Jakob Wirbel, Pedro Cutillas, Julio Saez-Rodriguez)....Pages 103-132 Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research (Stefka Tyanova, Juergen Cox)....Pages 133-148 Quantitative Analysis of Tyrosine Kinase Signaling Across Differentially Embedded Human Glioblastoma Tumors (Hannah Johnson, Forest M. White)....Pages 149-164 Front Matter ....Pages 165-165 Prediction of Clinical Endpoints in Breast Cancer Using NMR Metabolic Profiles (Leslie R. Euceda, Tonje H. Haukaas, Tone F. Bathen, Guro F. Giskeødegård)....Pages 167-189 Front Matter ....Pages 191-191 Stochastic and Deterministic Models for the Metastatic Emission Process: Formalisms and Crosslinks (Christophe Gomez, Niklas Hartung)....Pages 193-224 Mechanically Coupled Reaction-Diffusion Model to Predict Glioma Growth: Methodological Details (David A. Hormuth II, Stephanie L. Eldridge, Jared A. Weis, Michael I. Miga, Thomas E. Yankeelov)....Pages 225-241 Profiling Tumor Infiltrating Immune Cells with CIBERSORT (Binbin Chen, Michael S. Khodadoust, Chih Long Liu, Aaron M. Newman, Ash A. Alizadeh)....Pages 243-259 Systems Biology Approaches in Cancer Pathology (Aaron DeWard, Rebecca J. Critchley-Thorne)....Pages 261-273 Front Matter ....Pages 275-275 Bioinformatics Approaches to Predict Drug Responses from Genomic Sequencing (Neel S. Madhukar, Olivier Elemento)....Pages 277-296 A Robust Optimization Approach to Cancer Treatment under Toxicity Uncertainty (Junfeng Zhu, Hamidreza Badri, Kevin Leder)....Pages 297-331 Modeling of Interactions between Cancer Stem Cells and their Microenvironment: Predicting Clinical Response (Mary E. Sehl, Max S. Wicha)....Pages 333-349 Methods for High-throughput Drug Combination Screening and Synergy Scoring (Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio et al.)....Pages 351-398 Back Matter ....Pages 399-402