• The Basics of Microarrays
• 42 min
  1. How to design a successful microarray experiment

  • Dr. Rainer Breitling
• Microarrays in the Understanding of the Biology of the Cell and Whole Organism
• 51 min
  2. Genome-wide mapping of estrogen: receptor binding sites and activity

  • Prof. Jason Carroll
• Microarrays in the Diagnosis, Prognosis and Treatment of Disease
• 35 min
  3. Single nucleotide polymorphism microarrays in the analysis of cancer

  • Dr. Rameen Beroukhim
• Archived Lectures *These may not cover the latest advances in the field
• 23 min
  4. The use of statistics in microarray studies

  • Dr. Ernst Wit
• 42 min
  5. Simultaneous microarray measurement of nuclear and whole cell changes in gene expression reveals overlapping but distinct patterns of transcriptional regulation

  • Dr. Chris Cheadle
• 38 min
  6. Global analysis of gene translation

  • Prof. Philip Tofilon
• 36 min
  7. Microarrays in the study of the basic mechanisms of evolution

  • Dr. Greg Gibson
• 41 min
  8. The use of microarrays to understand the biology and toxicology of low dose arsenic

  • Prof. Joshua Hamilton
• 46 min
  9. The bioinformatics of microarrays

  • Dr. Maureen Sartor
• 44 min
  10. Genome-wide profiling of microRNAs: from scientist benchside to patient bedside

  • Prof. George Calin
• 42 min
  11. Microarrays: their design and use

  • Prof. Craig R. Tomlinson
• 67 min
  12. Cancer systems biology: dissection and analysis of context-specific molecular interaction networks

  • Prof. Andrea Califano
• 35 min
  13. Utilizing microarrays to study posttranscriptional regulatory mechanisms of plants

  • Dr. Brian Gregory

Printable Handouts

PDF

Navigable Slide Index

1. Introduction
2. Gene expression microarrays
3. Many types of microarrays
4. Gene lists publishing is long gone
5. Microarray analysis pipeline
6. What is the bioinformatics of microarrays
7. Clustering: identify co-expression patterns
8. Example of clustering heatmap
9. Distance measures and clustering methods
10. Hierarchical clustering
11. Simple, free, user-friendly clustering program
12. Advanced clustering methods
13. Example of clustering
14. Example of biclustering
15. Classification methods
16. Principal components analysis (PCA)
17. Discriminant analysis
18. Support vector machines (SVM)
19. Enrichment testing (1)
20. Enrichment testing (2)
21. Free programs using enrichment testing method
22. Free programs using other methods
23. Aspects to enrichment testing
24. Choosing the gene list or significance scores
25. What is the correct null set?
26. Choose the test to use for enrichment
27. Types of gene sets
28. Structure of GO
29. Adjust the resulting p-values
30. Data mining/pathway analysis/protein interactions
31. Helpful literature tools
32. Other bioinformatics tools
33. MiMI (1)
34. MiMI (2)
35. MiMI plugin for Cytoscape (1)
36. MiMI plugin for Cytoscape (2)
37. GIN (1)
38. GIN (2)
39. BioSearch 2D (1)
40. BioSearch 2D (2)
41. Sharing your data
42. Public repositories
43. Making use of microarray databases
44. Integrating data sources is key to understanding
45. Example of integration (1)
46. Example of Integration (2)
47. Thank you and acknowledgements

Topics Covered

• Overview of microarrays
• Clustering microarray data
• Clustering distance measures
• Clustering methods
• Classification methods
• Gene set enrichment testing
• Data mining, pathway, and protein interaction software
• Literature mining tools
• Examples of bioinformatics software tools
• Sharing your data: MIAME
• Microarray databases
• Integration of data

Links

Series:

• Microarrays

Categories:

• Methods

Talk Citation

Publication History

• Published on March 30, 2009
• Archived on February 25, 2021

Financial Disclosures

• Dr. Maureen Sartor has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.