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Intro

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Testing. Biological verification. and interpretation. Microarray experiment. Description ... use your results from ex.3 to evaluate your hypotheses from ex.1 ... – PowerPoint PPT presentation

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Title: Intro


1
lab 1
  • Intro
  • materials

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

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

8
lab 1 - exercise 1
lab 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
metabolic chart
lab 1
PFK2
PDC1
ALD2
10
lab1 - exercise 2
lab 1
  • 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
lab 1
  • Describe the result for the marked locus!
  • Draw a qualitative expression profile diagram
    by hand!

12
lab 1 - exercise 3
lab 1
  • 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 Risis 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 Risis 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 rlt1 - and give a negative sign !!
14
lab 1 - exercise 4
lab 1
  • 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_at_ebc.uu.se
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