Next Generation Microarray Bioinformatics

Methods and Protocols

Editors:

ISBN: 978-1-61779-399-8 (Print) 978-1-61779-400-1 (Online)

Table of contents (26 protocols)

previous Page of 2
  1. Front Matter

    Pages i-xvi

  2. INTRODUCTION AND RESOURCES FOR MICROARRAY BIOINFORMATICS

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 3-17

      A Primer on the Current State of Microarray Technologies

    3. No Access

      Book Protocol

      Pages 19-39

      The KEGG Databases and Tools Facilitating Omics Analysis: Latest Developments Involving Human Diseases and Pharmaceuticals

    4. No Access

      Book Protocol

      Pages 41-53

      Strategies to Explore Functional Genomics Data Sets in NCBI’s GEO Database

  3. MICROARRAY DATA ANALYSIS (TOP DOWN APPROACH)

    1. Front Matter

      Pages 55-55

    2. No Access

      Book Protocol

      Pages 57-72

      Analyzing Cancer Samples with SNP Arrays

    3. No Access

      Book Protocol

      Pages 73-85

      Classification Approaches for Microarray Gene Expression Data Analysis

    4. No Access

      Book Protocol

      Pages 87-100

      Biclustering of Time Series Microarray Data

    5. No Access

      Book Protocol

      Pages 101-112

      Using the Bioconductor GeneAnswers Package to Interpret Gene Lists

    6. No Access

      Book Protocol

      Pages 113-121

      Analysis of Isoform Expression from Splicing Array Using Multiple Comparisons

    7. No Access

      Book Protocol

      Pages 123-139

      Functional Comparison of Microarray Data Across Multiple Platforms Using the Method of Percentage of Overlapping Functions

    8. No Access

      Book Protocol

      Pages 141-155

      Performance Comparison of Multiple Microarray Platforms for Gene Expression Profiling

    9. No Access

      Book Protocol

      Pages 157-182

      Integrative Approaches for Microarray Data Analysis

  4. MICROARRAY BIOINFORMATICS IN SYSTEMS BIOLOGY (BOTTOM UP APPROACH)

    1. Front Matter

      Pages 183-183

    2. No Access

      Book Protocol

      Pages 185-197

      Modeling Gene Regulation Networks Using Ordinary Differential Equations

    3. No Access

      Book Protocol

      Pages 199-213

      Nonhomogeneous Dynamic Bayesian Networks in Systems Biology

    4. No Access

      Book Protocol

      Pages 215-233

      Inference of Regulatory Networks from Microarray Data with R and the Bioconductor Package qpgraph

    5. No Access

      Book Protocol

      Pages 235-246

      Effective Non-linear Methods for Inferring Genetic Regulation from Time-Series Microarray Gene Expression Data

  5. NEXT GENERATION SEQUENCING DATA ANALYSIS

    1. Front Matter

      Pages 247-247

    2. No Access

      Book Protocol

      Pages 249-257

      An Overview of the Analysis of Next Generation Sequencing Data

    3. No Access

      Book Protocol

      Pages 259-274

      How to Analyze Gene Expression Using RNA-Sequencing Data

    4. No Access

      Book Protocol

      Pages 275-291

      Analyzing ChIP-seq Data: Preprocessing, Normalization, Differential Identification, and Binding Pattern Characterization

    5. No Access

      Book Protocol

      Pages 293-303

      Identifying Differential Histone Modification Sites from ChIP‐seq Data

    6. No Access

      Book Protocol

      Pages 305-322

      ChIP-Seq Data Analysis: Identification of Protein–DNA Binding Sites with SISSRs Peak-Finder

previous Page of 2