1. 4.1 (Part 1) Flow diagram for gene expression profiling

2. 4.1 (Part 2) Flow diagram for gene expression profiling

3. 4.2 Common experimental designs for microarray analysis

4. 4.3 (Part 1) Principle of cDNA microarrays

5. 4.3 (Part 2) Principle of cDNA microarrays

6. 4.4 Types of printing pins

7. 4.5 Principle of oligonucleotide arrays

8. 4.6 (Part 1) Construction of oligonucleotide arrays

9. 4.6 (Part 2) Construction of oligonucleotide arrays

10. 4.7 (Part 1) Three methods for labeling cDNA

11. 4.7 (Part 2) Three methods for labeling cDNA

12. 4.8 Microarray images produced with a pin-and-loop arrayer

13. 4.9 Simple normalization of microarray data

14. 4.10 Analysis of variance (ANOVA) for gene expression data

15. 4.11 Volcano plot of significance against effect

16. 4.12 Hierarchical clustering of gene expression

17. 4.13 Profile plots

18. 4.14 (Part 1) Chromatin immunoprecipitation and regulatory pathways

19. 4.14 (Part 2) Chromatin immunoprecipitation and regulatory pathways

20. 4.15 (Part 1) Principle of SAGE

21. 4.15 (Part 2) Principle of SAGE

22. 4.16 (Part 1) SAGE analysis of yeast and colorectal cancer transcriptomes

23. 4.16 (Part 2) SAGE analysis of yeast and colorectal cancer transcriptomes

24. 4.17 (Part 1) Microbead-based gene expression profiling

25. 4.17 (Part 2) Microbead-based gene expression profiling

26. 4.17 (Part 3) Microbead-based gene expression profiling

27. 4.18 (Part 1) Quantitative RT-PCR

28. 4.18 (Part 2) Quantitative RT-PCR

29. 4.18 (Part 3) Quantitative RT-PCR

30. 4.19 (Part 1) Microarray analysis of sporulation in budding yeast

31. 4.19 (Part 2) Microarray analysis of sporulation in budding yeast

32. 4.20 Gene expression changes in yeast

33. 4.21 The compendium approach

34. 4.22 (Part 1) Molecular pharmacology of cancers

35. 4.22 (Part 2) Molecular pharmacology of cancers

36. 4.22 (Part 3) Molecular pharmacology of cancers

37. 4.22 (Part 4) Molecular pharmacology of cancers

38. 4.22 (Part 5) Molecular pharmacology of cancers

39. 4.23 (Part 1) Microarray analysis and the etiology of Sandhoff and Tay-Sachs diseases

40. 4.23 (Part 2) Microarray analysis and the etiology of Sandhoff and Tay-Sachs diseases

41. 4.23 (Part 3) Microarray analysis and the etiology of Sandhoff and Tay-Sachs diseases

42. 4.24 (Part 1) Developmental changes in gene expression in Drosophila

43. 4.24 (Part 2) Developmental changes in gene expression in Drosophila

44. 4.25 (Part 1) Divergence in gene expression in primates

45. 4.25 (Part 2) Divergence in gene expression in primates

46. 4.25 (Part 3) Divergence in gene expression in primates

47. 4.26 (Part 1) Expression quantitative trait loci (eQTL)

48. 4.26 (Part 2) Expression quantitative trait loci (eQTL)

49. 4.27 Flow diagram of microarray database queries

50. Box 4.1 Microarray Image Processing

51. Box 4.2 Basic Statistical Methods

52. Exercise 4.1 (Part 1) Design a Microarray Experiment

53. Exercise 4.1 (Part 2) Design a Microarray Experiment

54. Exercise 4.1 (Part 3) Design a Microarray Experiment

55. Exercise 4.1 (Part 4) Design a Microarray Experiment

56. Exercise 4.2 (Part 1) Calculate which genes are differentially expressed

57. Exercise 4.2 (Part 2) Calculate which genes are differentially expressed

58. Exercise 4.3 Evaluate the significance of the following gene expression differences

59. Exercise 4.4 Perform a cluster analysis on gene expression profiles