DNA Methylation Microarrays —— Experimental Design and Statistical Analysis

----- DNA 甲基化微序：试验设计与统计分析

ISBN: 9781420067279 出版年：2008 页码：258 Wang, Sun-Chong Petronis, Art CRC Press

Preface Applied Statistics Descriptive statistics Inferential statistics DNA Methylation Microarrays and Quality Control DNA methylation microarrays Workflow of methylome experiment Image analysis Visualization of raw data Reproducibility Experimental Design Goals of experiment Reference design Balanced block design Loop design Factorial design Time course experimental design How many samples/arrays are needed? Appendix Data Normalization Measure of methylation The need for normalization Strategy for normalization Two-color CpG island microarray normalization Oligonucleotide arrays normalization Normalization using control sequences Appendix Significant Differential Methylation Fold change Linear model for log-ratios or log-intensities t test for contrasts F test for joint contrasts P-value adjustment for multiple testing Modified t and F tests Significant variation within and between groups Significant correlation with a covariate Permutation test for bisulfite sequence data Missing data values Appendix High-Density Genomic Tiling Arrays Normalization Wilcoxon test in a sliding window Boundaries of methylation regions Multiscale analysis by wavelets Unsupervised segmentation by hidden Markov model Principal component analysis and biplot Cluster Analysis Measure of dissimilarity Dimensionality reduction Hierarchical clustering K-means clustering Model-based clustering Quality of clustering Statistical significance of clusters Reproducibility of clusters Repeated measurements Statistical Classification Feature selection Discriminant function K-nearest neighbor Performance assessment Interdependency Network of DNA Methylation Graphs and networks Partial correlation Dependence networks from DNA methylation microarrays Network analysis Time Series Experiment Regulatory networks from microarray data Dynamic model of regulation A penalized likelihood score for parsimonious model Optimization by genetic algorithms Online Annotations Gene centric resources PubMeth: A cancer methylation database Gene Ontology Kyoto Encyclopedia of Genes and Genomes UniProt/Swiss-Prot protein knowledgebase The International HapMap Project UCSC human genome browser Public Microarray Data Repositories Epigenetics Society Microarray Gene Expression Data Society Minimum Information About a Microarray Experiment Public repositories for high-throughput arrays Open Source Software for Microarray Data Analysis R: A language and environment for statistical computing and graphics Bioconductor References Index