Analysis of genomic and proteomic data - e-learning |
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  • Introduction
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  • česky| english
  • 1. Introduction
  • 2. Data analysis
    • 2.1. General analysis workflow
      • 2.1.1. Data pre-processing
      • 2.1.2. Class comparison (searching for differences between classes)
        • 2.1.2.1. Calculation of effect sizes
        • 2.1.2.2. Hypothesis testing
          • 2.1.2.2.1. Methods for hypothesis testing
        • 2.1.2.3. Regression strategies
      • 2.1.3. Class discovery (finding new groups)
        • 2.1.3.1.Distance based methods
          • 2.1.3.1.1. Defining similarity and distance metrics
          • 2.1.3.1.2. Hierarchical methods
          • 2.1.3.1.3. Non-hierarchical methods
        • 2.1.3.2. Model-based methods
        • 2.1.3.3 Video record of presentation: Supervised and unsupervised analysis, building predictors in microarrays
      • 2.1.4. Class prediction (predicting classes based on previous knowledge)
    • 2.2. Analysis of high-density genomic data
      • 2.2.1. DNA microarrays
        • 2.2.1.1. Basic principle of DNA microarrays
        • 2.2.1.2. Microarray production
        • 2.2.1.3. Types of microarrays
        • 2.2.1.4. Design of microarray experiments
        • 2.2.1.5. Data pre-processing
        • 2.2.1.6. Normalization
        • 2.2.1.7. Analysis of expression arrays
          • 2.2.1.7.1. Searching for differentially expressed genes
          • 2.2.1.7.2. Video record of presentation: Searching for differentially expressed genes
        • 2.2.1.8. Analysis of arrayCGH
          • 2.2.1.8.1. Methods based on segmentation respectively breakpoint detection
          • 2.2.1.8.2. Methods based on clustering
          • 2.2.1.8.3. Methods based on Hidden Markov Models
          • 2.2.1.8.4. Methods based on segmentation
          • 2.2.1.8.5. Methods searching for group-specific recurrent aberrations
          • 2.2.1.8.6. References
        • 2.2.1.9. Example
        • 2.2.1.10. Meta-analysis of microarray experiments
          • 2.2.1.10.1. Methods of meta-analysis of microarrays
          • 2.2.1.10.2. Software implementation of methods of meta-analysis
          • 2.2.1.10.3 Video record of presentation: Meta-analysis for omics datasets
          • 2.2.1.10.4. References
        • 2.2.1.11. Pathway Analysis
          • 2.2.1.11.1.Introduction
          • 2.2.1.11.2. Pathway and Gene Set Resources
          • 2.2.1.11.3 Gene Set and Pathway Analysis Methods
          • 2.2.1.11.4 Specific methods
          • 2.2.1.11.5 Discussion
          • 2.2.1.11.6 Video record of presentation: Pathway and gene set analysis of microarray data
          • 2.2.1.11.7 References
      • 2.2.2. DNA sequence analysis
        • 2.2.2.1 Video record of presentation: The State-of-the-Art in DNA Sequence Analysis
    • 2.3. Analysis of high-density proteomic data
      • 2.3.1. 2D-gel electrophoresis
        • 2.3.1.1. Pre-processing
        • 2.3.1.2. Analysis
      • 2.3.2. MASS spectrometry
        • 2.3.2.1. Introduction
        • 2.3.2.2. Statistical issues in the analysis of proteomic profiles
          • 2.3.2.2.1. Experimental Design
          • 2.3.2.2.2 Statistical analysis
        • 2.3.2.3. General conclusions
        • 2.3.2.4. Video record of presentation: Analysis of mass spectrometry protein data
        • 2.3.2.5. Acknowledgements and References
  • 3. Software
 
 
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