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2-D PAGE Map Analysis By Emilio Marengo

2-D PAGE Map Analysis by Emilio Marengo

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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;

2-D PAGE Map Analysis Summary

2-D PAGE Map Analysis: Methods and Protocols by Emilio Marengo

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.

About Emilio Marengo

Dr Elisa Robotti, PhD Dip. Scienze e Innovazione Tecnologica Universita del Piemonte Orientale Viale Michel 11 15121 Alessandria Tel: +39 0131 360272 Fax: +39 0131 360250 e-mail: [email protected] Emilio Marengo Department of Environmental and Life Sciences, University of Eastern Piedmont, Alessandria, Italy. [email protected]

Table of Contents

Part I: 2D-Maps Reproducibility and Maps Modeling

1. Sources of Experimental Variation in 2D-Maps: The Importance of Experimental Design in Gel-Based Proteomics
Cristina-Maria Valcu and Mihai Valcu

2. Decoding 2D-Maps by Autocovariance Functions
Maria Chiara Pietrogrande, Nicola Marchetti, and Francesco Dondi

3. Two-Dimensional Gel Electrophoresis Image Analysis via Dedicated Software Packages
Martin H. Maurer

Part II: Image Analysis Tools to Provide Spot Volume Datasets

4. Comparative Evaluation of Software Features and Performances
Daniela Cecconi

5. Image Pretreatment Tools I: Algorithms for Maps Denoising and Background Subtraction Methods
Carlo Vittorio Cannistraci and Massimo Alessio

6. Image Pretreatment Tools II: Normalization Techniques for 2DE and 2D-DIGE
Emilio Marengo and Elisa Robotti

7. Spot Matching of 2-DE Images Using Distance, Intensity, and Pattern Information
Hua-Mei Xin and Yuemin Zhu

8. Algorithms for Warping of 2D-PAGE Maps
Marcello Manfredi, Elisa Robotti, and Emilio Marnego

9. 2-DE Gel Analysis: The Spot Detection
Simona Martinotti and Elia Ranzato

10. GENOCOP Algorithm and Hierarchical Grid Transformation for Image Warping of Two Dimensional Gel Electrophoretic Maps
Elisa Robotti, Marco Demartini, and Emilio Marengo

11. Detection and Quantification of Protein Spots by Pinnacle
Jeffrey S. Morris and Howard B. Gutstein

12. A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots
Massimo Natale, Alfonso Caiazzo, and Elisa Ficarra

Part III: Statistical Methods Applied to Spot Volume Datasets to Identify Candidate Biomarkers

13. Multiple Testing and Pattern Recognition in 2DE Proteomics
Sebastien C. Carpentier

14. Chemometric Multivariate Tools for Candidate Biomarkers Identification: LDA, PLS-DA, SIMCA, Ranking-PCA
Elisa Robotti and Emilio Marengo

Part IV: Differential Analysis from Direct Image Analysis Tools

15. The Use of Legendre and Zernike Moment Functions for the Comparison of 2D-PAGE Maps
Elisa Robotti, Marco Demartini, and Emilio Marengo

16. Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data
Massimo Alessio and Carlo Vittorio Cannistraci

17. Differential Analysis of 2D-Maps by Pixel-Based Approaches
Emilio Marengo and Elisa Robotti

Additional information

2-D PAGE Map Analysis: Methods and Protocols by Emilio Marengo
Humana Press Inc.
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