Next generation microarray bioinformatics : methods and protocols / edited by Junbai Wang, Aik Choon Tan, Tianhai Tian. — New York : Humana Press ; Springer, c2012. – (58.17/M592/v.802)

Contents

    CONTENTS
    
    Preface
    Contributors
    PART I INTRODUCTION AND RESOURCES FOR MICROARRAY BIOINFORMATICS
    1 A Primer on the Current State of Microarray Technologies 3
    2 The KEGG Databases and Tools Facilitating Omics Analysis: Latest Developments Involving Human Diseases and Pharmaceuticals
    3 Strategies to Explore Functional Genomics Data Sets in NCBI's GEO Database 41
    PART II MICROARRAY DATA ANALYSIS (Top-Down APPROACH)
    4 Analyzing Cancer Samples with SNP Arrays
    5 Classification Approaches for Microarray Gene Expression Data Analysis
    6 Biclustering of Time Series Microarray Data
    7 Using the Bioconductor GeneAnswers Package to Interpret Gene Lists
    8 Analysis of Isoform Expression from Splicing Array Using Multiple Comparisons
    9 Functional Comparison of Microarray Data Across Multiple Platforms Using the Method of Percentage of Overlapping Functions 123
    10 Performance Comparison of Multiple Microarray Platforms for Gene Expression Profiling 141
    11 Integrative Approaches for Microarray Data Analysis 157
    PART III MICROARRY BIOINFORMATICS IN SYSTEMS BIOLOGY (BOTTOM- UP APPROACH )
    12 Modeling Gene Regulation Networks Using Ordinary Differential Equations
    13 Nonhomogeneous Dynamic Bayesian Networks in Systems Biology 199
    14 Inference of Regulatory Networks from Microarray Data with R and the Bioconductor Package qpgraph 215
    15 Effective Non-linear Methods for Inferring Genetic Regulation from Time-Series Microarray Gene Expression Data 235
    PART IV NEXT GENERATION SEQUENCING DATA ANALYSIS
    16 An Overview of the Analysis of Next Generation Sequencing Data
    17 How to Analyze Gene Expression Using RNA-Sequencing Data 259
    18 Analyzing ChIP-seq Data: Preprocessing， Normalization， Differential Identification， and Binding Pattern Characterization 275
    19 Identifying Differential Histone Modification Sites from ChIP-seq Data 293
    20 ChIP-Seq Data Analysis: Identification of Protein-DNA Binding Sites with SISSRs Peak-Finder 305
    21 Using ChIPMotifs for De Novo Motif Discovery of OCT4 and ZNF263 Based on ChiP-Based High-Throughput Experiments 323
    PART V EMERGING APPLICATIONS OF MICROARRAY AND NEXT GENERATION SEQUENCING
    22 Hidden Markov Models for Controlling False Discovery Rate in Genome-Wide Association Analysis
    23 Employing Gene Set Top Scoring Pairs to Identify Deregulated Pathway-Signatures in Dilated Cardiomyopathy from Integrated Microarray Gene Expression Data
    24 JAMIE: A Software Tool for Jointly Analyzing Multiple ChiP-chip Experiments
    25 Epigenetic Analysis: ChiP-chip and ChIP-seq
    26 BiNGS!SL-seq: A Bioinformatics Pipeline for the Analysis and Interpretation of Deep Sequencing Genome-Wide Synthetic Lethal Screen
    Index