1. 1 Intro & materials

2. 2 Overview Monday –MA experimental basic –MA data analysis –Introduction to lab 1 –lab 1 Tuesday –Introduction to lab 2 –lab 2 Bio-Informatic motivation

3. 3 Intro lab 1 Biological question Differentially expressed genes Classification etc. Testing Biological verification and interpretation Microarray experiment Description Experimental design Image analysis Normalization Clustering Discrimination lab 1

4. 4 de Risi et al, 1997 (Science) diauxic shift (yeast) Intro lab 1

5. 5 [2] [3] [4] 9h13h21h... [1] metabolic chart hypotheses hypotheses for regulation of ALD2, PDC1 and PFK2 Genes/time [h] 9111315 ALD2 1.141.181.151.35 PDC1 1.060.90.930.87 PFK2 1.141.111.350.97 table of results graph display of results & hypotheses comparison with hypotheses Intro lab 1 look on raw data!

6. 6 Intro lab 1 how to do the graphic display:

7. 7 Overview Monday –MA experimental basic –MA data analysis –Introduction to lab 1 –lab 1 Exercises 1-4 Tuesday –Introduction to lab 2 –lab 2 Bio-Informatic motivation

8. 8 lab 1 - exercise 1 examine the following metabolic chart! For each of the three enzymes marked with yellow arrows give a clear hypothesis about the dynamics of the belonging mRNA- levels during the diauxic shift in yeast! (which expression profiles do you expect?) Give your reasoning in each case, which makes your hypotheses plausible! lab 1

9. 9 metabolic chart PFK2 ALD2 PDC1 lab 1

10. 10 lab1 - exercise 2 de Risi et al (Science, 1997) assessed the mRNA levels during the diauxic shift via MicroArray - have a look at three of the raw data TIFF-files (following sheet)!de Risi et al (Science, 1997) Sum the experimental procedure (a few sentences) lab 1

11. 11 9h13h21h lab 1 Describe the result for the marked locus! Draw a qualitative expression profile diagram by hand!

12. 12 lab 1 - exercise 3 the following table gives you the numeric results for the three enzymes from ex. 1 as ratios r = Intensity(Red)/Intensity(Green) Enter these values as an Excel table! compare de Risi’s graphs in the figure on sheet 6 - and use Excel to produce a graph containing the expression profiles for these genes! (the graph should be as similar to de Risi’s as possible!) lab 1

13. 13 Genes/time [h] 9111315171921 ALD2 1.141.181.151.351.6412.54.76 PDC1 1.060.90.930.870.680.430.21 PFK2 1.141.111.350.970.980.50.39 Use these values of r (= Intensity(Red)/Intensity(Green)) to graphically display the expression profiles for ALD2, PDC1 and PFK2 (as similar to the graph on sheet 6 as you can) EXPLAIN: inverting those r<1 - and give a negative sign !! table of results lab 1

14. 14 lab 1 - exercise 4 use your results from ex.3 to evaluate your hypotheses from ex.1 (does everything look as expected ?) Try to find a reason for any unexpected detail! lab 1

15. 15 pass your results to Cecilia.Hansen@ebc.uu.se