2-D page map analysis
Subtitle: methods and protocols
By: edited by Emilio Marengo and Elisa Robotti, Department of Sciences and Technological Innovation, Universita del Piemonte Orientale, Alessandria, Italy
Series: Methods in molecular biology -- 1384
Published: 2016
Language: eng
Number of pages: 331
ISBN-13: 9781493932542; 9781493932559
Copyright date: 2016
Subjects: Methods; Principal Component Analysis; Proteomics; Two-dimensional electrophoresis; Statistical Models; Electrophoresis, Gel, Two-Dimensional; Image Processing, Computer-Assisted
Other titles: Two-dimensional page map analysis
Description: 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.
Notes: Includes bibliographical references and index.

Sources of experimental variation in 2-D maps : the importance of experimental design in gel-based proteomics / Cristina-Maria Valcu and Mihai Valcu -- Decoding 2-D maps by autocovariance function / Maria Chiara Pietrogrande, Nicola Marchetti, and Francesco Dondi -- Two-dimensional gel electrophoresis image analysis via dedicated software packages / Martin H. Maurer -- Comparative evaluation of software features and performances / Daniela Cecconi -- Image pretreatment tools I : algorithms for map denoising and background subtraction methods / Carlo Vittorio Cannistraci and Massimo Alessio -- Image pretreatment tools II : normalization techniques for 2-DE and 2-D DIGE / Elisa Robotti, Emilio Marengo, and Fabio Quasso -- Spot matching of 2-DE images using distance, intensity, and pattern information / Hua-Mei Xin and Yuemin Zhu -- Algorithms for warping of 2-D PAGE maps / Marcello Manfredi, Elisa Robotti, and Emilio Marengo -- 2-DE gel analysis : the spot detection / Simona Martinotti and Elia Ranzato -- GENOCOP algorithm and hierarchical grid transformation for image warping of two-dimensional gel electrophoretic maps / Elisa Robotti, Emilio Marengo, and Marco Demartini -- Detection and quantification of protein spots by pinnacle / Jeffrey S. Morris and Howard B. Gutstein -- Novel gaussian extrapolation approach for 2-D gel electrophoresis saturated protein spots / Massimo Natale, Alfonso Caiazzo, and Elisa Ficarra -- Multiple testing and pattern recognition in 2-DE proteomics / Sebastien C. Carpentier -- Chemometric multivariate tools for candidate biomarker identification : LDA, PLS-DA, SIMCA, ranking-PCA / Elisa Robotti and Emilio Marengo -- Use of legendre and zernike moment functions for the comparison of 2-D PAGE maps / Emilio Marengo, Elisa Robotti, and Marco Demartini -- Nonlinear dimensionality reduction by minimum curvilinearity for unsupervised discovery of patterns in multidimensional proteomic data / Massimo Alessio and Carlo Vittorio Cannistraci -- Differential analysis of 2-D maps by pixel-based approaches / Emilio Marengo, Elisa Robotti, and Fabio Quasso.
Table of contents: title: Sources of experimental variation in 2-D maps : the importance of experimental design in gel-based proteomics  -- Cristina-Maria Valcu and Mihai Valcu; title: Decoding 2-D maps by autocovariance function  -- Maria Chiara Pietrogrande, Nicola Marchetti, and Francesco Dondi; title: Two-dimensional gel electrophoresis image analysis via dedicated software packages  -- Martin H. Maurer; title: Comparative evaluation of software features and performances  -- Daniela Cecconi; title: Image pretreatment tools I : algorithms for map denoising and background subtraction methods  -- Carlo Vittorio Cannistraci and Massimo Alessio; title: Image pretreatment tools II : normalization techniques for 2-DE and 2-D DIGE  -- Elisa Robotti, Emilio Marengo, and Fabio Quasso; title: Spot matching of 2-DE images using distance, intensity, and pattern information  -- Hua-Mei Xin and Yuemin Zhu; title: Algorithms for warping of 2-D PAGE maps  -- Marcello Manfredi, Elisa Robotti, and Emilio Marengo; title: 2-DE gel analysis : the spot detection  -- Simona Martinotti and Elia Ranzato; title: GENOCOP algorithm and hierarchical grid transformation for image warping of two-dimensional gel electrophoretic maps  -- Elisa Robotti, Emilio Marengo, and Marco Demartini; title: Detection and quantification of protein spots by pinnacle  -- Jeffrey S. Morris and Howard B. Gutstein; title: Novel gaussian extrapolation approach for 2-D gel electrophoresis saturated protein spots  -- Massimo Natale, Alfonso Caiazzo, and Elisa Ficarra; title: Multiple testing and pattern recognition in 2-DE proteomics  -- Sebastien C. Carpentier; title: Chemometric multivariate tools for candidate biomarker identification : LDA, PLS-DA, SIMCA, ranking-PCA  -- Elisa Robotti and Emilio Marengo; title: Use of legendre and zernike moment functions for the comparison of 2-D PAGE maps  -- Emilio Marengo, Elisa Robotti, and Marco Demartini; title: Nonlinear dimensionality reduction by minimum curvilinearity for unsupervised discovery of patterns in multidimensional proteomic data  -- Massimo Alessio and Carlo Vittorio Cannistraci; title: Differential analysis of 2-D maps by pixel-based approaches -- Emilio Marengo, Elisa Robotti, and Fabio Quasso.