1. Gene Expression Analysis Gabor T. Marth Department of Biology, Boston College marth@bc.edu BI420 – Introduction to Bioinformatics

2. Gene expression

3. Why study gene expression? at different developmental stages? in cells of different tissues? at different time points in the same cell? cells under different environmental conditions? between normal and cancerous cells? Which genes are active

4. What are expression microarrays?

5. Expression microarrays – “physical appearance”

6. Microarray construction

7. cDNA preparation

8. Expression assay

9. Expression microarray movie http://www.bio.davidson.edu/Courses/genomics/chip/chip.html DNA microarray chip animation:

10. Chip readout – absolute expression and ratio

11. Chip readout – relative transcription

12. Chip readout – example

13. Time course experiments Experiment: measuring gene expression as oxygen gets depleted in yeast grown in a closed container

14. Time course data

15. Data analysis – normalization balance fluorescent intensities of two dyes adjust for differences in experimental conditions

16. Normalization

17. Log2 transformation Double or half expression now has the same magnitude

18. Clustering – intro Why: if the expression pattern for gene B is similar to gene A, maybe they are involved in the same or related pathway How: Re-order expression vectors in the data set so that similar patterns are together

19. Clustering – numerical

20. Clustering – visual

21. Hierarchical clustering: pair-wise similarity

22. Hierarchical clustering: cluster construction

23. Clustering – large example

24. Next two classes Chapter 7. Chapter 8.

25. Application of microarrays: classification of cancers

26. Microarrays to detect genome copy #

27. Protein identification Protein separation by 2D gel eletrophoresis

28. Protein identification mass spectrometry

29. Protein function identification protein chips: identification of proteins that bind specific chemicals

30. Thanks Olga Troyanskaya, Ph.D. Department of Computer Science Lewis-Sigler Institute for Integrative Genomics Princeton University Expression informatics slides courtesy of: