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2-D PAGE Map Analysis

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Cover of '2-D PAGE Map Analysis'

Table of Contents

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    Book Overview
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    Chapter 1 Sources of Experimental Variation in 2-D Maps: The Importance of Experimental Design in Gel-Based Proteomics
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    Chapter 2 Decoding 2-D Maps by Autocovariance Function
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    Chapter 3 Two-Dimensional Gel Electrophoresis Image Analysis via Dedicated Software Packages
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    Chapter 4 Comparative Evaluation of Software Features and Performances
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    Chapter 5 Image Pretreatment Tools I: Algorithms for Map Denoising and Background Subtraction Methods
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    Chapter 6 Image Pretreatment Tools II: Normalization Techniques for 2-DE and 2-D DIGE
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    Chapter 7 Spot Matching of 2-DE Images Using Distance, Intensity, and Pattern Information
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    Chapter 8 Algorithms for Warping of 2-D PAGE Maps
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    Chapter 9 2-DE Gel Analysis: The Spot Detection
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    Chapter 10 2-D PAGE Map Analysis
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    Chapter 11 Detection and Quantification of Protein Spots by Pinnacle
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    Chapter 12 A Novel Gaussian Extrapolation Approach for 2-D Gel Electrophoresis Saturated Protein Spots
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    Chapter 13 Multiple Testing and Pattern Recognition in 2-DE Proteomics
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    Chapter 14 Chemometric Multivariate Tools for Candidate Biomarker Identification: LDA, PLS-DA, SIMCA, Ranking-PCA
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    Chapter 15 The Use of Legendre and Zernike Moment Functions for the Comparison of 2-D PAGE Maps
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    Chapter 16 Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data
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    Chapter 17 Differential Analysis of 2-D Maps by Pixel-Based Approaches
Attention for Chapter 4: Comparative Evaluation of Software Features and Performances
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Chapter title
Comparative Evaluation of Software Features and Performances
Chapter number 4
Book title
2-D PAGE Map Analysis
Published in
Methods in molecular biology, January 2016
DOI 10.1007/978-1-4939-3255-9_4
Pubmed ID
26611409
Book ISBNs
978-1-4939-3254-2, 978-1-4939-3255-9
Authors

Daniela Cecconi

Abstract

Analysis of two-dimensional gel images is a crucial step for the determination of changes in the protein expression, but at present, it still represents one of the bottlenecks in 2-DE studies. Over the years, different commercial and academic software packages have been developed for the analysis of 2-DE images. Each of these shows different advantageous characteristics in terms of quality of analysis. In this chapter, the characteristics of the different commercial software packages are compared in order to evaluate their main features and performances.

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