1

Intro

&

materials

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

Intro lab 1Biological question

Differentially expressed genesClassification etc.

Testing

Biological verification and interpretation

Microarray experiment

Description

Experimental design

Image analysis

Normalization

Clustering Discrimination

lab 1

4

de Risi et al, 1997 (Science)

diauxic shift (yeast)

Intro lab 1

5

[2]

[3]

[4]

9h 13h 21h

. . .

[1]metabolic chart

hypotheseshypotheses for regulation ofALD2, PDC1 and PFK2

Genes/time [h] 9 11 13 15

ALD2 1.14 1.18 1.15 1.35

PDC1 1.06 0.9 0.93 0.87

PFK2 1.14 1.11 1.35 0.97

table of results

graph display of results &comparison with hypotheseshypotheses

Intro lab 1

look on raw data!

6

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

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

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

metabolic chart

PFK2

ALD2

PDC

1

lab 1

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 theraw data TIFF-files (following sheet)!

• Sum the experimental procedure (a few sentences)

lab 1

11

9h 13h 21h

lab 1

• Describe the result for the marked locus!

• Draw a qualitative expression profile diagram by hand!

12

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!)

lab 1

13

Genes/time [h] 9 11 13 15 17 19 21

ALD2 1.14 1.18 1.15 1.35 1.64 12.5 4.76

PDC1 1.06 0.9 0.93 0.87 0.68 0.43 0.21

PFK2 1.14 1.11 1.35 0.97 0.98 0.5 0.39

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

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

pass your results

to

Cecilia.Hansen@ebc.uu.se