Skip to main content
SpringerLink
Log in
Book cover

Protein Networks and Pathway Analysis

  • Book
  • © 2009

Overview

Editors:
  1. Yuri Nikolsky

    1. GeneGo Inc., Encinitas, U.S.A.

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Julie Bryant

    1. GeneGo Inc., Encinitas, U.S.A.

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • A broad overview of experimental and analytical methods of functional data analysis written by the leaders in the field
  • Details multiple aspects of biological networks, from collecting binary interactions to building algorithms and modeling
  • Provides a guide to real life and research applications of current methods of systems biology
  • Covers a wide range of cell-based assay formats and systems
  • Presents a modular approach to experimental design, covering model biological systems, screening modalities, detection technologies, and approaches to data analysis
  • Comprehensive guide to developing, running, and analyzing cell-based assays in high-throughput screening
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 563)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 119.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (20 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Part I: Interactions

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Mining Protein–Protein Interactions from Published Literature Using Linguamatics I2E

      • Judith Bandy, David Milward, Sarah McQuay
      Pages 3-13

    3. Relative Avidity, Specificity, and Sensitivity of Transcription Factor–DNA Binding in Genome-Scale Experiments

      • Vladimir A. Kuznetsov
      Pages 15-50

    4. Curation of Inhibitor-Target Data: Process and Impact on Pathway Analysis

      • Sreenivas Devidas
      Pages 51-62

    5. Profiling Protein Interaction Networks with Functional Protein Microarrays

      • Dawn R. Mattoon, Barry Schweitzer
      Pages 63-74

    6. Manual Annotation of Protein Interactions

      • Svetlana Bureeva, Svetlana Zvereva, Valentin Romanov, Tatiana Serebryiskaya
      Pages 75-95

  3. Part II: Analysis

    1. Front Matter

      Pages 97-97
      Download chapter PDF

    2. Gene Set Enrichment Analysis

      • Charles A. Tilford, Nathan O. Siemers
      Pages 99-121

    3. PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools

      • Huaiyu Mi, Paul Thomas
      Pages 123-140

    4. Prioritizing Genes for Pathway Impact Using Network Analysis

      • Aaron N. Chang
      Pages 141-156

    5. Discovering Biological Networks from Diverse Functional Genomic Data

      • Chad L. Myers, Camelia Chiriac, Olga G. Troyanskaya
      Pages 157-175

    6. Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated “Knowledge-Based” Platform

      • Yuri Nikolsky, Eugene Kirillov, Roman Zuev, Eugene Rakhmatulin, Tatiana Nikolskaya
      Pages 177-196

    7. Kinetic Modeling as a Tool to Integrate Multilevel Dynamic Experimental Data

      • Ekaterina Mogilevskaya, Natalia Bagrova, Tatiana Plyusnina, Nail Gizzatkulov, Eugeniy Metelkin, Ekaterina Goryacheva et al.
      Pages 197-218

    8. Cytoscape: A Community-Based Framework for Network Modeling

      • Sarah Killcoyne, Gregory W. Carter, Jennifer Smith, John Boyle
      Pages 219-239

    9. Semantic Data Integration and Knowledge Management to Represent Biological Network Associations

      • Sascha Losko, Klaus Heumann
      Pages 241-258

    10. Solutions for Complex, Multi Data Type and Multi Tool Analysis: Principles and Applications of Using Workflow and Pipelining Methods

      • Robin E. J. Munro, Yike Guo
      Pages 259-271

  4. Part III: Applications

    1. Front Matter

      Pages 273-273
      Download chapter PDF

    2. High-Throughput siRNA Screening as a Method of Perturbation of Biological Systems and Identification of Targeted Pathways Coupled with Compound Screening

      • Jeff Kiefer, Hongwei H. Yin, Qiang Q. Que, Spyro Mousses
      Pages 275-287

    3. Pathway and Network Analysis with High-Density Allelic Association Data

      • Ali Torkamani, Nicholas J. Schork
      Pages 289-301
Back to top

Keywords

About this book

From the beginning of the OMICs biology era, science has been pursuing the reduction of the complex "genome-wide" assays in order to understand the essential biology that lies beneath it. In Protein Networks and Pathway Analysis, expert practitioners present a compilation of methods of functional data analysis, often referred to as "systems biology," and its applications in drug discovery, medicine and basic disease research. The volume is divided into three convenient sections, covering the elucidation of protein, compound and gene interactions, analytical tools, including networks, interactome and ontologies, and applications of functional analysis. As a volume in the highly successful Methods in Molecular Biology™ series, this work provides detailed descriptions and hands-on implementation advice. Authoritative and cutting-edge, Protein Networks and Pathway Analysis presents both "wet lab" experimental methods and computational tools in order to cover a broad spectrum of issues in this fascinating new field.

Editors and Affiliations

  • GeneGo Inc., Encinitas, U.S.A.

    Yuri Nikolsky, Julie Bryant

Bibliographic Information

  • Book Title: Protein Networks and Pathway Analysis

  • Editors: Yuri Nikolsky, Julie Bryant

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-60761-175-2

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2009

  • Hardcover ISBN: 978-1-60761-174-5Published: 28 July 2009

  • Softcover ISBN: 978-1-61779-488-9Published: 01 December 2011

  • eBook ISBN: 978-1-60761-175-2Published: 14 July 2009

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 410

  • Number of Illustrations: 118 b/w illustrations

  • Topics: Protein Science, Computer Appl. in Life Sciences

  • Industry Sectors: Biotechnology, Pharma

Publish with us

Policies and ethics

Back to top

Search

Navigation