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Cancer Systems Biology

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Louise von Stechow

    1. NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

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  • Includes cutting-edge methods and Protocols
  • Provides step-by-step detail essential for reproducibles results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1711)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
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  2. Systems Biology of the Cancer Genetic and Epigenetic Landscape

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity Analysis

      • Hua Tan, Xiaobo Zhou
      Pages 3-11

    3. Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data

      • Amanda J. Kedaigle, Ernest Fraenkel
      Pages 13-26

    4. Analyzing DNA Methylation Patterns During Tumor Evolution

      • Heng Pan, Olivier Elemento
      Pages 27-53

    5. MicroRNA Networks in Breast Cancer Cells

      • Andliena Tahiri, Miriam R. Aure, Vessela N. Kristensen
      Pages 55-81

    6. Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels

      • James Campbell, Colm J. Ryan, Christopher J. Lord
      Pages 83-99Open Access

  3. Systems Analyses of Signaling Networks in Cancer Cells

    1. Front Matter

      Pages 101-101
      Download chapter PDF

    2. Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells

      • Jakob Wirbel, Pedro Cutillas, Julio Saez-Rodriguez
      Pages 103-132Open Access

    3. Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research

      • Stefka Tyanova, Juergen Cox
      Pages 133-148Open Access

    4. Quantitative Analysis of Tyrosine Kinase Signaling Across Differentially Embedded Human Glioblastoma Tumors

      • Hannah Johnson, Forest M. White
      Pages 149-164

  4. Systems Analysis of Cancer Cell Metabolism

    1. Front Matter

      Pages 165-165
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    2. Prediction of Clinical Endpoints in Breast Cancer Using NMR Metabolic Profiles

      • Leslie R. Euceda, Tonje H. Haukaas, Tone F. Bathen, Guro F. GiskeødegÃ¥rd
      Pages 167-189

  5. Systems Biology of Metastasis and Tumor/Microenvironment Interactions

    1. Front Matter

      Pages 191-191
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    2. Stochastic and Deterministic Models for the Metastatic Emission Process: Formalisms and Crosslinks

      • Christophe Gomez, Niklas Hartung
      Pages 193-224

    3. 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

    4. Profiling Tumor Infiltrating Immune Cells with CIBERSORT

      • Binbin Chen, Michael S. Khodadoust, Chih Long Liu, Aaron M. Newman, Ash A. Alizadeh
      Pages 243-259

    5. Systems Biology Approaches in Cancer Pathology

      • Aaron DeWard, Rebecca J. Critchley-Thorne
      Pages 261-273

  6. Modeling Drug Responses in Cancer Cells

    1. Front Matter

      Pages 275-275
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    2. Bioinformatics Approaches to Predict Drug Responses from Genomic Sequencing

      • Neel S. Madhukar, Olivier Elemento
      Pages 277-296
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Keywords

About this book

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 Analysisof 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.


Editors and Affiliations

  • NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

    Louise von Stechow

Bibliographic Information

  • Book Title: Cancer Systems Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Louise von Stechow

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7493-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7492-4Published: 18 January 2018

  • Softcover ISBN: 978-1-4939-8503-6Published: 04 June 2019

  • eBook ISBN: 978-1-4939-7493-1Published: 17 January 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 402

  • Number of Illustrations: 10 b/w illustrations, 76 illustrations in colour

  • Topics: Cancer Research

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