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2-D PAGE Map Analysis

Methods and Protocols

  • Book
  • © 2016

Overview

Editors:
  1. Emilio Marengo

    1. Department of Sciences and Technological Innovation, Università del Piemonte Orientale, Alessandria, Italy

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    You can also search for this editor in PubMed   Google Scholar

  2. Elisa Robotti

    1. Department of Sciences and Technological Innovation, Università del Piemonte Orientale , Alessandria, Italy

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1384)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xvi
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  2. 2D-Maps Reproducibility and Maps Modeling

    1. Front Matter

      Pages 1-1
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    2. Sources of Experimental Variation in 2-D Maps: The Importance of Experimental Design in Gel-Based Proteomics

      • Cristina-Maria Valcu, Mihai Valcu
      Pages 3-37

    3. Decoding 2-D Maps by Autocovariance Function

      • Maria Chiara Pietrogrande, Nicola Marchetti, Francesco Dondi
      Pages 39-53

    4. Two-Dimensional Gel Electrophoresis Image Analysis via Dedicated Software Packages

      • Martin H. Maurer
      Pages 55-65

  3. Image Analysis Tools to Provide Spot Volume Datasets

    1. Front Matter

      Pages 67-67
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    2. Comparative Evaluation of Software Features and Performances

      • Daniela Cecconi
      Pages 69-78

    3. Image Pretreatment Tools I: Algorithms for Map Denoising and Background Subtraction Methods

      • Carlo Vittorio Cannistraci, Massimo Alessio
      Pages 79-89

    4. Image Pretreatment Tools II: Normalization Techniques for 2-DE and 2-D DIGE

      • Elisa Robotti, Emilio Marengo, Fabio Quasso
      Pages 91-107

    5. Spot Matching of 2-DE Images Using Distance, Intensity, and Pattern Information

      • Hua-Mei Xin, Yuemin Zhu
      Pages 109-117

    6. Algorithms for Warping of 2-D PAGE Maps

      • Marcello Manfredi, Elisa Robotti, Emilio Marengo
      Pages 119-154

    7. 2-DE Gel Analysis: The Spot Detection

      • Simona Martinotti, Elia Ranzato
      Pages 155-164

    8. GENOCOP Algorithm and Hierarchical Grid Transformation for Image Warping of Two-Dimensional Gel Electrophoretic Maps

      • Elisa Robotti, Emilio Marengo, Marco Demartini
      Pages 165-184

    9. Detection and Quantification of Protein Spots by Pinnacle

      • Jeffrey S. Morris, Howard B. Gutstein
      Pages 185-201

    10. A Novel Gaussian Extrapolation Approach for 2-D Gel Electrophoresis Saturated Protein Spots

      • Massimo Natale, Alfonso Caiazzo, Elisa Ficarra
      Pages 203-211

  4. Statistical Methods Applied to Spot Volume Datasets to Identify Candidate Biomarkers

    1. Front Matter

      Pages 213-213
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    2. Multiple Testing and Pattern Recognition in 2-DE Proteomics

      • Sebastien C. Carpentier
      Pages 215-235

    3. Chemometric Multivariate Tools for Candidate Biomarker Identification: LDA, PLS-DA, SIMCA, Ranking-PCA

      • Elisa Robotti, Emilio Marengo
      Pages 237-267

  5. Differential Analysis from Direct Image Analysis Tools

    1. Front Matter

      Pages 269-269
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    2. The Use of Legendre and Zernike Moment Functions for the Comparison of 2-D PAGE Maps

      • Emilio Marengo, Elisa Robotti, Marco Demartini
      Pages 271-288
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Keywords

About this book

Exploring the 2-D gel mapping field, the chapters in this book are separated into four different categories: Part I talks about 2-D maps reproducibility and maps modeling; Part II describes the image analysis tools that provide spot volume datasets; Part III is about the statistical methods applied to spot volume datasets to identify candidate biomarkers; and Part IV discusses differential analysis from direct image analysis tools. 2-D PAGE Map Analysis: Methods and Protocols provides a unique approach to 2-D gel mapping, in that it helps users avoid drawbacks due to ignorance of the basic theoretical mechanisms underlying the technique, including data handling and proper tools for spot analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, 2-D PAGE Map Analysis: Methods and Protocols, is a useful resource for any scientist or researcher, with a mathematical background, who is interested in 2-D gel mapping.

Editors and Affiliations

  • Department of Sciences and Technological Innovation, Università del Piemonte Orientale, Alessandria, Italy

    Emilio Marengo

  • Department of Sciences and Technological Innovation, Università del Piemonte Orientale , Alessandria, Italy

    Elisa Robotti

About the editors

Dr Elisa Robotti, PhD Dip. Scienze e Innovazione Tecnologica Università del Piemonte Orientale Viale Michel 11 15121 Alessandria Tel: +39 0131 360272 Fax: +39 0131 360250 e-mail: elisa.robotti@mfn.unipmn.it Emilio Marengo Department of Environmental and Life Sciences, University of Eastern Piedmont, Alessandria, Italy. marengoe@tin.it

Bibliographic Information

  • Book Title: 2-D PAGE Map Analysis

  • Book Subtitle: Methods and Protocols

  • Editors: Emilio Marengo, Elisa Robotti

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3255-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3254-2Published: 27 November 2015

  • Softcover ISBN: 978-1-4939-4949-6Published: 23 August 2016

  • eBook ISBN: 978-1-4939-3255-9Published: 26 November 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 331

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

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