Keywords:
Proteins -- Analysis -- Data processing -- Congresses.
;
Electronic books.
Type of Medium:
Online Resource
Pages:
1 online resource (285 pages)
Edition:
1st ed.
ISBN:
9789401792028
Series Statement:
Translational Bioinformatics Series ; v.6
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=1802583
DDC:
572.6
Language:
English
Note:
Intro -- Preface -- Contents -- Chapter 1: Introduction to Genomics and Proteomics for Clinical Discovery and Development -- 1.1 1.1 Genomics and Proteomics for Clinical Discovery and Development -- 1.2 1.2 The ENCODE Project -- 1.3 1.3 HPP - The Human Proteome Project -- 1.4 1.4 Personalized Medicine -- 1.5 1.5 Biobanking -- References -- Chapter 2: Identification of Missing Proteins: Toward the Completion of Human Proteome -- 2.1 Introduction -- 2.2 Current State of Human Protein Project -- 2.3 Methods for Identification -- 2.4 Databases -- 2.5 Application of Selected Reaction Monitoring Mass Spectrometry -- 2.6 Conclusions -- References -- Chapter 3: Chromosome Transcriptome Profiling in the Context of High-Throughput Proteomics Studies -- 3.1 Introduction -- 3.2 Bioinformatics Methods in Proteogenomics -- 3.2.1 Databases for Annotation of Genes and Proteins -- 3.2.2 Analysis of Whole Transcriptome Experiments -- 3.2.2.1 Microarray Data Analysis -- 3.2.2.2 Next-Generation Sequencing Data Analysis -- 3.2.3 Analysis of Whole Proteome Experiments -- 3.3 Chromosome Transcriptome Profiling Oriented Towards Proteome Research -- 3.3.1 C-HPP Genome Annotation -- 3.3.2 Whole Transcriptome Profiling Using Microarrays -- 3.3.3 Extension of the Chromosome Transcriptome Profiling with RNA-Seq Data -- 3.3.3.1 Tissue Specific Expression of Human Genes -- 3.3.3.2 In-Depth Analysis of Missing Proteins -- 3.4 Summary -- References -- Chapter 4: Standards for Proteomics Data Dissemination and Experiments Reporting -- 4.1 Background: Basic Principles -- 4.2 Data Standards: HUPO-PSI-XML, MIAPEs and CVS -- 4.2.1 Reporting Guidelines: Minimal Information About a Proteomic Experiment (MIAPE Documents) -- 4.2.2 The Extensible Markup Language (XML) to Standardize Proteomics Data Storage -- 4.2.3 Controlled Vocabularies.
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4.3 Repositories for Proteomics and Biological Data -- 4.3.1 MS-Based Data: ProteomeXchange Consortium -- 4.3.1.1 PRIDE ( http://www.ebi.ac.uk/pride/) -- 4.3.1.2 PeptideAtlas ( http://www.peptideatlas.org/) -- 4.3.1.3 Global Protein Machine Database - GPM/gpmDB ( http://www.thegpm.org/) -- 4.3.2 Proteomics Data Submission to Public Repositories -- 4.3.3 Proteomics Related Data: Human Resources -- 4.3.3.1 Universal Protein Resource Knowledge Base, UniProtKB ( http://www.uniprot.org/) -- 4.3.3.2 National Center for Biotechnology Information, NCBI ( http://www.ncbi.nlm.nih.gov) -- 4.3.3.3 A Knowledge Platform for Human Proteins: neXtprot ( http://www.nextprot.org/) -- 4.3.3.4 The Human Protein Atlas ( http://www.proteinatlas.org/) -- 4.3.3.5 The Human Protein Reference Database HPRD ( http://www.hprd.org/) -- 4.4 Tools for Automatic Data Retrieving -- 4.4.1 Genomics and Transcriptomic Data: Babelomics, GeneCodis -- 4.4.2 Genomics and Proteomics Enrichment: DAVID -- 4.4.3 Proteomics Data Integration: PIKE -- 4.5 Example Using PIKE -- 4.5.1 How to Start? -- 4.5.2 Entering Your Query -- 4.5.3 Showing the Results -- 4.5.4 Poring Over the Data -- 4.5.5 Integrating the Results -- 4.6 Conclusions -- References -- Chapter 5: Mass Spectrometry-Based Protein Sequencing Platforms -- 5.1 Introduction -- 5.2 MS-Based Sequencing of Polypeptides -- 5.2.1 Collision-Induced Dissociation (CID) (Paizs and Suhai 2005) -- 5.2.1.1 Charge-Directed Fragmentation Pathways -- 5.2.1.2 Charge-Remote Fragmentations -- 5.2.2 Electron-Transfer Dissociation (ETD) -- 5.2.2.1 Direct Dissociation-Like Cleavage of N-C α Bond -- 5.2.2.2 Decision Tree (DT)-Driven Shotgun Sequencing -- 5.2.2.3 Peptide Sequencing by Dual Fragmentation (Frese et al. 2012) -- 5.3 LC/MS-Based Shotgun Cancer Proteomics -- 5.3.1 Proteolysis Prior to Sequencing Proteins.
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5.3.2 Sample Preparations of Clinical Specimens -- 5.3.2.1 Plasma Samples -- 5.3.2.2 FFPE Tissue Specimens -- 5.3.3 Differential Protein Expression Analysis -- 5.4 Bioinformatics for Sequence Identification -- 5.4.1 Database Search Approach -- 5.4.2 Spectral-Library Matching Approach (Tharakan et al. 2010 -- Ning et al. 2010 -- Ahrne et al. 2009) -- 5.4.3 De novo Spectrum Sequencing (Seidler et al. 2010 -- Frank et al. 2007 -- Pan et al. 2010 -- Frank and Pevzner 2005 -- Ma et al. 2003 -- Tanner et al. 2005 -- Dasari et al. 2010) -- 5.4.4 Sequence-Tag/Hybrid Approaches -- 5.4.5 Statistical Confidence on Peptide Identification -- 5.4.5.1 False Discovery Rate (FDR) -- 5.4.5.2 Machine Learning Methods -- 5.4.6 Protein Inference Problem (Nesvizhskii and Aebersold 2005 -- Nesvizhskii 2010 -- Li and Radivojac 2012) -- 5.5 Perspectives -- References -- Chapter 6: Post-translational Modifications in the Human Proteome -- 6.1 Introduction -- 6.2 Protein Acetylation -- 6.3 Protein Phosphorylation -- 6.4 Protein Glycosylation -- 6.5 Protein Ubiquitination -- 6.6 Lipid Modifications of Proteins -- 6.7 Inference of PTMs from MS Data -- 6.8 Summary -- References -- Chapter 7: Biomarker Discovery Utilizing Biobanking Archives and the Diagnostic Market -- 7.1 7.1 Introduction -- 7.2 7.2 Biomarkers and Diagnostics -- 7.3 7.3 Clinical Diagnostics and Treatment for Research -- 7.4 7.4 Biobanking -- 7.5 7.5 Biomarker Discovery -- References -- Chapter 8: Protein Microarrays: Overview, Applications and Challenges -- 8.1 Introduction -- 8.2 Protein Microarrays -- 8.3 Array Format -- 8.3.1 Planar Array -- 8.3.1.1 Array Chemistries -- 8.3.1.2 Array Printing -- 8.3.1.3 Assay Execution -- 8.3.1.4 Assay Detection -- 8.3.2 Beads Arrays -- 8.4 Content -- 8.4.1 Assembled Arrays -- 8.4.1.1 Antibody Arrays -- Assembled Array Signal Detection -- 8.4.2 Reverse-Phase Arrays.
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8.4.3 Self-Assembled Protein Microarrays -- 8.4.3.1 In Situ Protein Expression Systems -- 8.5 Types of In Situ Protein Arrays -- 8.5.1 PISA -- 8.5.2 DAPA -- 8.5.3 PuCA -- 8.5.4 NAPPA -- 8.6 Applications of NAPPA Arrays -- 8.6.1 NAPPA Arrays for Vaccine Development -- 8.6.2 NAPPA for Protein-Protein Interaction -- 8.6.3 NAPPA Arrays for Detecting Autoimmune Response -- 8.7 Conclusions and Future Directions -- References -- Chapter 9: Clinical Bioinformatics: A New Emerging Science of Biomarker Development -- 9.1 Introduction -- 9.2 Significance of Clinical Bioinformatics -- 9.3 Introduction of Systems Clinical Medicine -- 9.4 Biomarkers, Network Biomarkers, and Dynamic Network Biomarkers -- 9.5 Applied Methodologies -- 9.6 Development and Application of DESS -- References -- Chapter 10: Rapid Advances in the Field of Epigenetics -- 10.1 Epigenetic Regulation -- 10.1.1 What Is Epigenome? -- 10.1.2 X-Inactivation and Genomic Imprinting -- 10.1.3 Structure of Chromatin and Epigenetic Modification -- 10.1.4 DNA Modification -- 10.1.5 Histone Modification and Variants -- 10.1.6 RNA -- 10.1.7 Polycomb and Trithorax -- 10.1.8 Xist and Heterochromatin Formation -- 10.1.9 Reprogramming -- 10.1.10 Cell Division -- 10.1.11 Retrotransposon -- 10.1.12 None-Histone Target of Epigenetic Enzyme -- 10.1.13 Vitamin -- 10.1.14 Infection -- 10.2 Approach for Epigenetic Analysis -- 10.2.1 Introduction -- 10.2.2 Epigenetic Regulators as Drug Targets -- 10.2.3 Epigenome Associated Protein Complex as Drug Target -- 10.2.4 Development of Epigenetic Regulator Inhibitor -- 10.2.5 Analysis with Next Generation DNA Sequencer (NGS) -- 10.2.6 Analysis with Mass Spectrometry -- 10.2.6.1 Chemistry of Histone -- 10.2.6.2 Sample Preparation -- 10.2.6.3 High Performance Liquid Chromatography (HPLC) -- 10.2.6.4 Mass Spectrometry (MS) -- 10.2.6.5 Tandem Mass Spectrometry (MS/MS).
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10.2.6.6 Database Search -- 10.2.6.7 Quantification -- 10.2.6.8 Analysis of Histone H4 and H3 Tails -- 10.2.6.9 Perspective -- 10.2.7 Summary -- References -- Chapter 11: Pharmacogenomics in Drug Development -- 11.1 Introduction -- 11.2 Determinants of Drug Disposition -- 11.3 Drug Metabolizing Phase I Enzymes and Polymorphism -- 11.3.1 CYP2D6 -- 11.3.2 CYP2C19 -- 11.3.3 CYP2C9 -- 11.4 Drug Metabolizing Phase II Enzymes and Polymorphism -- 11.5 Drug Transporters and Polymorphism -- 11.5.1 OATP1B1 -- 11.6 Pharmacogenomics in Drug Development -- 11.7 Concluding Remarks and Future Perspectives -- References -- Chapter 12: The Role of Proteomics in the Development of Personalized Medicine, Diagnostic Methods and Large Scale Biobanking -- 12.1 12.1 Introduction -- 12.2 12.2 Biobanking - Regulatory Aspects -- 12.3 12.3 Patient Donors and Sample Integrity -- 12.4 12.4 Proteomics in Clinical Diagnostics - Analytical Aspects -- 12.5 12.5 Concluding Remarks -- References -- Chapter 13: Imaging Techniques in Proteomics Research -- 13.1 Introduction -- 13.2 Mass Spectrometry Imaging (MSI) -- 13.3 Matrix-Assisted Laser Desorption Ionization (MALDI)-MSI -- 13.4 Secondary Ion Mass Spectrometry (SIMS) Imaging -- 13.5 Desorption Electro Spray Ionization (DESI) Imaging -- 13.6 Rapid Evaporative Ionization Mass Spectrometry (REIMS) Imaging -- 13.7 Targets in MSI -- 13.7.1 MSI of Peptides and Proteins -- 13.7.2 MSI of Lipids -- 13.7.3 MSI of Pharmaceuticals -- 13.7.4 MSI of Neurotransmitters and Endogenous Metabolites -- 13.7.5 MSI of Inorganic Ions -- 13.8 MSI Data Analysis Software -- 13.8.1 Open MSI -- 13.9 Conclusion and Future Perspectives -- References -- Index.
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