Data Analysis Tools for DNA Microarrays
Data Analysis Tools for DNA Microarrays
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DOI：
10.1201/9780203486078
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发表时间：
2003-06
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影响因子：
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通讯作者：
S. Drăghici
中科院分区：
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作者：
S. Drăghici
前言生物信息学-一门新兴学科基因组信息的构建基因信息的表达对微阵列的需求微阵列-基因表达分析工具微阵列的制作微阵列的应用微阵列在基因表达研究中的应用挑战变异性来源图像处理简介数字成像的基本要素微阵列图像处理cDNA微阵列图像处理亲和微阵列的处理统计学基础介绍一些基本术语基本统计概率贝叶斯定理概率分布中心极限定理重复有用吗？摘要解决的问题练习统计假设检验介绍框架假设检验和显著性“我不相信上帝不存在”假设检验的算法假设检验中的错误解决的问题经典方法数据分析介绍测试涉及单样本测试涉及两个样本练习方差分析-方差分析介绍单因素方差分析两个-方法方差分析质量控制练习实验设计实验设计的概念比较品种改进生产过程实验设计原则实验设计指南统计实验设计的简短综合一些微阵列特定实验设计多重比较介绍多重比较的问题更多多重比较的精确参数校正分析和可视化工具介绍箱形图基因饼散点图直方图时间序列主成分分析（PCA）独立成分分析（伊卡）聚类分析介绍度量距离分层聚类k均值聚类Kohonen映射（SOFM）数据预处理和归一化介绍一般预处理处理技术cDNA数据特有的标准化问题亲和素数据特有的标准化问题亲和素数据标准化的其他方法处理和标准化序列附录选择差异调节基因的方法介绍标准倍数变化异常比率假设检验，多重比较和回归方差分析的校正基于噪声采样模型的最大似然估计方法亲和比较调用其他方法附录微阵列数据的功能分析和生物学解释介绍基因本体论其他相关资源翻译差异调节基因列表Into Biological Knowledge Onto-Express摘要聚焦微阵列-比较和选择介绍阵列选择的标准Onto-Compare一些比较商业应用介绍使用GeneSight进行组间显著性检验使用S-PLUS和Insightful ArrayAnalyzer SAS软件进行基因组学微阵列数据的统计分析Spofire的决策网站未来之路下一步是什么？分子诊断基因调控网络
PREFACE INTRODUCTION Bioinformatics - An Emerging Discipline The Building Blocks of Genomic Information Expression of Genetic Information The Need for Microarrays MICROARRAYS Microarrays - Tools for Gene Expression Analysis Fabrication of Microarrays Applications of Microarrays Challenges in Using Microarrays in Gene Expression Studies Sources of Variability IMAGE PROCESSING Introduction Basic Elements of Digital Imaging Microarray Image Processing Image Processing of cDNA Microarrays Image Processing of Affymetrix Microarrrays ELEMENTS OF STATISTICS Introduction Some Basic Terms Elementary Statistics Probabilities Bayes' Theorem Probability Distributions Central Limit Theorem Are Replicates Useful? Summary Solved Problems Exercises STATISTICAL HYPOTHESIS TESTING Introduction The framework Hypothesis Testing and Significance "I Do Not Believe God Does Not Exist" An Algorithm for Hypothesis Testing Errors in Hypothesis Testing Solved Problems CLASSICAL APPROACHES TO DATA ANALYSIS Introduction Tests Involving a Single Sample Tests Involving Two Samples Exercises ANALYSIS OF VARIANCE - ANOVA Introduction One-Way ANOVA Two-Way ANOVA Quality Control Exercises EXPERIMENT DESIGN The Concept of Experiment Design Comparing Varieties Improving the Production Process Principles of Experimental Design Guidelines for Experimental Design A Short Synthesis of Statistical Experiment Designs Some Microarray Specific Experiment Designs MULTIPLE COMPARISONS Introduction The Problem of Multiple Comparisons A More Precise Argument Corrections for Multiple Comparisons ANALYSIS AND VISUALIZATION TOOLS Introduction Box Plots Gene Pies Scatter Plots Histograms Time Series Principal Component Analysis (PCA) Independent Component Analysis (ICA) CLUSTER ANALYSIS Introduction Metric Distances Hierarchical Clustering k-Means Clustering Kohonen Maps (SOFM) DATA PRE-PROCESSING AND NORMALIZATION Introduction General Pre-Processing Techniques Normalization Issues Specific to cDNA Data Normalization Issues Specific to Affymetrix Data Other Approaches to the Normalization of Affymetrix Data Useful Pre-Processing and Normalization Sequences Appendix METHODS FOR SELECTING DIFFERENTIALLY REGULATED GENES Introduction Criteria Fold Change Unusual Ratio Hypothesis Testing, Corrections for Multiple Comparisons and Resampling ANOVA Noise Sampling Model Based Maximum Likelihood Estimation Methods Affymetrix Comparison Calls Other Methods Appendix FUNCTIONAL ANALYSIS AND BIOLOGICAL INTERPRETATION OF MICROARRAY DATA Introduction The Gene Ontology Other Related Resources Translating Lists of Differentially Regulated Genes into Biological Knowledge Onto-Express Summary FOCUSED MICROARRAYS - COMPARISON AND SELECTION Introduction Criteria for Array Selection Onto-Compare Some Comparisons COMMERCIAL APPLICATIONS Introduction Significance Testing Among Groups Using GeneSight Statistical Analysis of Microarray Data Using S-PLUS and Insightful ArrayAnalyzer SAS Software for Genomics Spofire's Decision Site THE ROAD AHEAD What Next? Molecular Diagnosis Gene Regulatory Networks Conclusions REFERENCES