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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. - PowerPoint PPT Presentation
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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
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metabolic chart
PFK2
ALD2
PDC
1
lab 1
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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
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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