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E-raamat: Statistical Analysis in Proteomics

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This valuable collection aims to provide a collection of frequently used statistical methods in the field of proteomics. Although there is a large overlap between statistical methods for the different ‘omics’ fields, methods for analyzing data from proteomics experiments need their own specific adaptations. To satisfy that need, Statistical Analysis in Proteomics focuses on the planning of proteomics experiments, the preprocessing and analysis of the data, the integration of proteomics data with other high-throughput data, as well as some special topics. Written for the highly successful Methods in Molecular Biology series, the chapters contain the kind of detail and expert implementation advice that makes for a smooth transition to the laboratory.

Practical and authoritative, Statistical Analysis in Proteomics serves as an ideal reference for statisticians involved in the planning and analysis of proteomics experiments, beginners as well as advanced researchers, and also for biologists, biochemists, and medical researchers who want to learn more about the statistical opportunities in the analysis of proteomics data.

Preface v
Contributors ix
Part I Proteomics, Study Design, and Data Processing
1 Introduction to Proteomics Technologies
3(26)
Christof Lenz
Hassan Dihazi
2 Topics in Study Design and Analysis for Multistage Clinical Proteomics Studies
29(34)
Irene Sui Lan Zeng
3 Preprocessing and Analysis of LC-MS-Based Proteomic Data
63(14)
Tsung-Heng Tsai
Minkun Wang
Habtom W. Ressom
4 Normalization of Reverse Phase Protein Microarray Data: Choosing the Best Normalization Analyte
77(14)
Antonella Chiechi
5 Outlier Detection for Mass Spectrometric Data
91(14)
HyungJun Cho
Soo-Heang Eo
Part II Group Comparisons
6 Visualization and Differential Analysis of Protein Expression Data Using R
105(14)
Tome S. Silva
Nadege Richard
7 False Discovery Rate Estimation in Proteomics
119(10)
Suruchi Aggarwal
Amit Kumar Yadav
8 A Nonparametric Bayesian Model for Nested Clustering
129(14)
Juhee Lee
Peter Muller
Yitan Zhu
Yuan Ji
9 Set-Based Test Procedures for the Functional Analysis of Protein Lists from Differential Analysis
143(16)
Jochen Kruppa
Klaus Jung
Part III Classification Methods
10 Classification of Samples with Order-Restricted Discriminant Rules
159(16)
David Conde
Miguel A. Fernandez
Bonifacio Salvador
Cristina Rueda
11 Application of Discriminant Analysis and Cross-Validation on Proteomics Data
175(10)
Julia Kuligowski
David Perez-Guaita
Guillermo Quintas
12 Protein Sequence Analysis by Proximities
185(14)
Frank-Michael Schleif
Part IV Data Integration
13 Statistical Method for Integrative Platform Analysis: Application to Integration of Proteomic and Microarray Data
199(10)
Xin Gao
14 Data Fusion in Metabolomics and Proteomics for Biomarker Discovery
209(18)
Lionel Blanchet
Agnieszka Smolinska
Part V Special Topics
15 Reconstruction of Protein Networks Using Reverse-Phase Protein Array Data
227(20)
Silvia von der Heyde
Johanna Sonntag
Frank Kramer
Christian Bender
Ulrike Korf
Tim Beißbarth
16 Detection of Unknown Amino Acid Substitutions Using Error-Tolerant Database Search
247(18)
Sven H. Giese
Franziska Zickmann
Bernhard Y. Renard
17 Data Analysis Strategies for Protein Modification Identification
265(12)
Yan Fu
18 Dissecting the iTRAQ Data Analysis
277(16)
Suruchi Aggarwal
Amit Kumar Yadav
19 Statistical Aspects in Proteomic Biomarker Discovery
293(18)
Klaus Jung
Index 311