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Functional genomics (II): Common technologies and data analysis methods

• Introduction

• Real-time PCR

• Microarrays

  • Counteracting dye bias effects when using two-colour arrays
  • Analysis of microarray data
    • Feature extraction
    • Quality control
    • Normalisation
    • Differential expression analysis
    • Biological interpretation of gene expression data
    • Submission of data to a public repository
  • Limitations of microarrays

• Next Generation Sequencing (NGS)

  • RNA sequencing
  • Biological interpretation of gene expression data
    • Gene set enrichment analysis and pathway analysis
  • Genotyping, epigenetic and DNA/RNA-protein interaction method
  • Epigenetic modifications
    • Histone modifications
  • DNA/RNA-protein interactions