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DNA Microarrays DNA Microarrays Purpose • Measure the activity of thousands

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									DNA Microarrays
                   Purpose
• Measure the activity of thousands of genes at
  the same time

• Have a plate that has the genes on it

• You then add your sample to see if it hybridizes
  with any of the genes

• Other techniques that we have studied only
  allows you to study one or a few genes are the
  same time
  Genes are differentially regulated
• All somatic cells in an organism contain the same genes

• Different genes are expressed in different tissues under
  different conditions

• Different tissues have different functions because
  different genes are expressed

• In some tissues, different genes may be expressed at
  different times in development
 High vs. low expression of genes
• It is not always best to have high
  expression of genes
  – What would be an example in cancer?
  – What genes would you not want to be
    expressed?
  – What genes would you want to be expressed?
DNA chip = microarray = gene chip
         = genome chip
• Have a slide
  – Imprinted with a pattern of spots
  – Each spot has many copies of a specific
    sequence representing a gene
      Quick overview of procedure
• Have two different groups – look at genes that
  are up or down regulated or absent

•   Isolate mRNA
•   make cDNAs
•   Tag the DNA with dyes so they can be detected
•   Add the labeled DNA to the slides
•   Analyze if hybridization took place – computer
    analysis
 Mock DNA microarray experiment
• Use a DNA microarray to study expression of 6
  different genes
• Normal lung cells vs. cancerous lung cells

• 4 different types of genes:
  – Some genes transcribed less in cancer than in normal
    cells
  – Some genes transcribed more in cancer than in
    normal cells
  – Some genes transcribed at the same level
  – Some genes are not expressed at all in normal or
    cancerous lung cells
            Compare data
• Control vs. patient
• Indication of who might have genes
  involved in cancer
  – What are the genes that cause cancer
                  Colors
• If you had red, green and yellow, which
  color would be the mix of the other two
  colors?

• If you had pink, purple and blue, which
  color would be the mix of the other two
  colors?
         Color interpretation
• You do not always get genes that are
  highly expressed or highly repressed,
  there may be intermediary colors

• For example, dark red may indicate a
  gene that is highly expressed but if it is a
  light red, it might be only slightly
  expressed
  We will use the color scheme below to
     quantitate our results from our
          microarray experiment




Ratio = gene expression in cancer cells/gene expression in normal cells

Which range of numbers indicate expression in cancer cells but not in normal
Cells?
Which range of numbers indicate expression in normal cells but not in cancer
Cells?
Which range of numbers indicate expression in both normal cells and cancer
cells?
Are there numbers where there is expression in neither normal nor cancer cells?

								
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