Brain Transcriptome

1st Edition, Volume 116 - August 26, 2014
Latest edition
Editors: Robert Hitzemann, Shannon Mcweeney
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 0 1 1 0 5 - 8
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 0 1 3 1 9 - 9

Published since 1959, International Review of Neurobiology is a well-known series appealing to neuroscientists, clinicians, psychologists, physiologists, and pharmacol… Read more

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Published since 1959, International Review of Neurobiology is a well-known series appealing to neuroscientists, clinicians, psychologists, physiologists, and pharmacologists. Led by an internationally renowned editorial board, this important serial publishes both eclectic volumes made up of timely reviews and thematic volumes that focus on recent progress in a specific area of neurobiology research.

This volume, concentrates on the brain transcriptome.

Chapter One: Introduction to Sequencing the Brain Transcriptome
- Abstract
- 1 Introduction
- 2 From Microarrays to RNA-Seq
- 3 NGS Platforms
- 4 RNA-Seq Overview
- 5 RNA-Seq and Data Analysis
- 6 Sequencing the Brain Transcriptome
- 7 Conclusions
- Acknowledgments
Chapter Two: Analysis Considerations for Utilizing RNA-Seq to Characterize the Brain Transcriptome
- Abstract
- 1 Introduction
- 2 Defining and Quantifying Transcript/Gene Expression
- 3 Detecting Differential Expression
- 4 Frameworks for Interpretation
- 5 Summary
Chapter Three: Data Integration and Reproducibility for High-Throughput Transcriptomics
- Abstract
- 1 Opportunities for Secondary Use of Data and Meta-Anlaysis in Transcriptomics
- 2 Selecting the Unit of Comparison
- 3 Metrics for Agreement
- 4 Studies on Reproducibility and Validation
- 5 Guidelines for Cross-Platform Studies
- 6 Other Data Integration Considerations
- 7 Summary
Chapter Four: Coexpression and Cosplicing Network Approaches for the Study of Mammalian Brain Transcriptomes
- Abstract
- 1 Introduction
- 2 Construction of Coexpression and Cosplicing Networks
- 3 Cosplicing Network Construction
- 4 Biological Annotation of Coexpression and Cosplicing Networks
- 5 Effects of Genetic Selection on Gene Networks
- 6 Module Preservation Across Subpopulations and Species
- 7 Module Disruption Related to Behavioral Changes
- 8 Summary and Future Directions
Chapter Five: Splicing in the Human Brain
- Abstract
- 1 Pre-mRNA Splicing in Human Cells
- 2 Alternative Pre-mRNA Splicing
- 3 Tissue-Specific Alternative Splicing
- 4 Alternative Splicing in the Brain
- 5 Brain-Specific Splicing Regulation
- 6 Transcription-Coupled Regulation of Alternative Splicing
- 7 Cotranscriptional and Posttranscriptional Splicing
- 8 Global Analysis of Pre-mRNA Splicing
- 9 The Influence of RNA Extraction Methods on Transcriptome Analysis
- 10 Computational Methods to Study Splicing Dynamics
Chapter Six: Understanding Complex Transcriptome Dynamics in Schizophrenia and Other Neurological Diseases Using RNA Sequencing
- Abstract
- 1 Introduction
- 2 RNA-Seq Studies on Neurological Disorders
- 3 Quantifying Transcriptome Dynamics in Neurological Disorders
- 4 Discussion and Perspectives
Chapter Seven: The Central Role of Noncoding RNA in the Brain
- Abstract
- 1 Introduction
- 2 The Long and Short of Noncoding RNAs
- 3 Types and Function of lncRNAs
- 4 RNA Structure
- 5 Splicing
- 6 NcRNA Editing
- 7 Epigenetic Modifications
- 8 ncRNAs Are Involved in Neuronal Development, Maintenance, and Plasticity
- 9 Evolutionary Role of ncRNAs and Primate Specificity
- 10 The Role of (Retro)transposons and Pseudogenes in ncRNA Evolution
- 11 ncRNAs and Disease
- 12 Perspectives and Outlook
- Acknowledgments
Chapter Eight: Genetics of Gene Expression in CNS
- Abstract
- 1 Introduction
- 2 Genetic Resources for eQTL Analysis in Mice
- 3 Genetic Mapping Methods
- 4 RNA-seq eQTL Studies
- 5 Pros and Cons of Arrays and RNA-seq for eQTL Studies
- 6 RNA-seq Read Alignment and Normalization
- 7 eQTL Mapping of Alternative Splicing and Polyadenylation
- 8 RNA-seq for Allele-Specific Expression
- 9 Conclusions
- Acknowledgments
Chapter Nine: Transcriptomic Changes in Brain Development
- Abstract
- 1 Introduction
- 2 Gene Expression
- 3 DNA Sequence Variation and Epigenetic Modification in Brain Development
- 4 Alternative Splicing
- 5 RNA Editing
- 6 Noncoding RNA
- 7 Summary
Chapter Ten: Gene Expression in the Addicted Brain
- Abstract
- 1 Introduction
- 2 Molecular Adaptations Accompanying Early Response and Long-Term Adaptations in the Addicted Brain
- 3 Substance-Specific and Shared Gene Expression Changes in Addicted Brain
- 4 Region-Specific Gene Expression Changes in Addicted Brain
- 5 Perturbation of the Glutamatergic System in Addicted Brain
- 6 Epigenetic Regulation of Gene Expression in Addicted Brain
- 7 Conclusion
Chapter Eleven: RNA-Seq Reveals Novel Transcriptional Reorganization in Human Alcoholic Brain
- Abstract
- 1 Overview
- 2 RNA-Seq of Postmortem Brain Tissue
- 3 Detection of Technical Biases in RNA-Seq Data
- 4 Normalization of RNA-Seq Data
- 5 Alternative Splicing and Differential Expression
- 6 Long Noncoding RNA
- 7 Novel Three Prime Untranslated Regions
- 8 Genetic Variation and Alcohol Dependence
- 9 Biological Coexpression Networks
- 10 Future Directions
Index
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Brain Transcriptome

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Robert Hitzemann

Shannon Mcweeney

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