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Intro & materials

lab 1. Intro & materials. Monday MA experimental basic MA data analysis Introduction to lab 1 lab 1. Tuesday Introduction to lab 2 lab 2. Overview. Bio-Informatic motivation. Intro lab 1. Biological question Differentially expressed genes Classification etc.

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Intro & materials

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  1. lab 1 Intro & materials

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

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

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

  5. 21h Intro lab 1 [1] metabolic chart hypotheses for regulation of ALD2, PDC1 and PFK2 9h 13h [2] look on raw data! . . . [3] table of results [4] graph display of results & comparison with hypotheses

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

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

  8. lab 1 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!

  9. lab 1 metabolic chart PFK2 PDC1 ALD2

  10. lab 1 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 theraw data TIFF-files (following sheet)! • Sum the experimental procedure (a few sentences)

  11. 9h 13h 21h lab 1 • Describe the result for the marked locus! • Draw a qualitative expression profile diagram by hand!

  12. lab 1 lab 1 - exercise 3 • the following table gives you the numeric results for the three enzymes from ex. 1as 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!)

  13. lab 1 table of results 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 !!

  14. lab 1 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!

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

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