Microarrays for an Integrative Genomics (Paperback)
暫譯: 整合基因組學的微陣列技術 (平裝本)

Isaac S. Kohane, Alvin Kho, Atul J. Butte

  • 出版商: MIT
  • 出版日期: 2005-08-12
  • 售價: $775
  • 語言: 英文
  • 頁數: 326
  • 裝訂: Paperback
  • ISBN: 0262612100
  • ISBN-13: 9780262612104
  • 相關分類: 生物資訊 BioinformaticsData Science
  • 立即出貨 (庫存 < 4)

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商品描述

Description:

Functional genomics--the deconstruction of the genome to determine the biological function of genes and gene interactions--is one of the most fruitful new areas of biology. The growing use of DNA microarrays allows researchers to assess the expression of tens of thousands of genes at a time. This quantitative change has led to qualitative progress in our ability to understand regulatory processes at the cellular level.

This book provides a systematic introduction to the use of DNA microarrays as an investigative tool for functional genomics. The presentation is appropriate for readers from biology or bioinformatics. After presenting a framework for the design of microarray-driven functional genomics experiments, the book discusses the foundations for analyzing microarray data sets, genomic data-mining, the creation of standardized nomenclature and data models, clinical applications of functional genomics research, and the future of functional genomics.

Isaac S. Kohane is Director of the Children’s Hospital Informatics Program, Associate Professor of Pediatrics at Harvard Medical School, and an Attending Physician in Endocrinology at Children's Hospital, Boston.

Alvin Kho is Research Fellow in Medicine at Children's Hospital, Boston.

Atul J. Butte is a Staff Informatician in the Children's Hospital Informatics Program, an Instructor in Pediatrics at Harvard Medical School, and an Attending Physician in Endocrinology at Children's Hospital, Boston.

 

Table of Contents:

Foreword xi
Preface xiii
Acknowledgments xvii
1 Introduction 1
1.1 The Future Is So Bright... 1
1.2 Functional Genomics 4
1.3 Missing the Forest for the Dendrograms 13
1.4 Functional Genomics, Not Genetics 19
1.5 Basic Biology 25
2 Experimental Design 37
2.1 The Safe Conception of a Functional Genomic Experiment 37
2.2 Gene-Clustering Dogma 60
3 Microarray Measurements to Analyses 69
3.1 Generic Features of Microarray Technologies 69
3.2 Replicate Experiments, Reproducibility, and Noise 88
3.3 Prototypical Objectives and Questions 116
3.4 Preprocessing: Filters and Normalization 121
3.5 Background on Fold 127
3.6 Dissimilarity and Similarity Measures 137
4 Genomic Data-Mining Techniques 149
4.1 Introduction 149
4.2 What Can Be Clustered in Functional Genomics? 149
4.3 What Does it Mean to Cluster? 150
4.4 Hierarchy of Bioinformatics Algorithms 151
4.5 Data Reduction and Filtering 155
4.6 Self-Organizing Maps 161
4.7 Finding Genes That Split Sets 169
4.8 Phylogenetic-Type Trees 172
4.9 Relevance Networks 181
4.10 Other Methods 189
4.11 Which Technique Should I Use? 191
4.12 Determining the Significance of Findings 195
4.13 Genetic Networks 203
5 Bio-Ontologies, Data Models, Nomenclature 215
5.1 Ontologies 216
5.2 Expressivity versus Computability 224
5.3 Ontology versus Data Model versus Nomenclature 226
5.4 Data Model Introduction 231
5.5 Nomenclature 239
5.6 Postanalysis Challenges 247
6 From Functional Genomics to Clinical Relevance 249
6.1 Electronic Medical Records 249
6.2 Standardized Vocabularies for Clinical Phenotypes 251
6.3 Privacy of Clinical Data 252
6.4 Costs of Clinical Data Acquisition 256
7 The Near Future 257
7.1 New Methods for Gene Expression Profiling 257
7.2 Respecting the Older Generation 266
7.3 Selecting Software 271
7.4 Investing in the Future of the Genomic Enterprise 273
Glossary 277
References 283
Index 296

商品描述(中文翻譯)

描述:
功能基因組學——對基因組的解構以確定基因及其相互作用的生物功能——是生物學中最具成果的新領域之一。DNA 微陣列的日益使用使研究人員能夠同時評估數萬個基因的表達。這一定量變化促進了我們在細胞層面理解調控過程的質量進步。

本書系統地介紹了 DNA 微陣列作為功能基因組學研究工具的使用。內容適合生物學或生物資訊學的讀者。在介紹微陣列驅動的功能基因組學實驗設計框架後,本書討論了分析微陣列數據集的基礎、基因組數據挖掘、標準化命名法和數據模型的創建、功能基因組學研究的臨床應用以及功能基因組學的未來。

Isaac S. Kohane 是波士頓兒童醫院資訊學計劃的主任,哈佛醫學院小兒科副教授,以及波士頓兒童醫院內分泌科的主治醫師。

Alvin Kho 是波士頓兒童醫院的醫學研究員。

Atul J. Butte 是波士頓兒童醫院資訊學計劃的資訊學員,哈佛醫學院小兒科講師,以及波士頓兒童醫院內分泌科的主治醫師。

目錄:
前言
序言
致謝
1 介紹
1.1 未來一片光明...
1.2 功能基因組學
1.3 迷失於樹狀圖
1.4 功能基因組學,而非遺傳學
1.5 基本生物學
2 實驗設計
2.1 功能基因組學實驗的安全構思
2.2 基因聚類教條
3 微陣列測量到分析
3.1 微陣列技術的通用特徵
3.2 重複實驗、可重複性與噪音
3.3 原型目標與問題
3.4 預處理:過濾與標準化
3.5 有關 Fold 的背景
3.6 不相似性與相似性度量
4 基因組數據挖掘技術
4.1 介紹
4.2 在功能基因組學中可以聚類的內容?
4.3 聚類意味著什麼?
4.4 生物資訊學算法的層次結構
4.5