01%20introduction%201_15_08

01%20introduction%201_15_08 - Central Dogma: DNA RNA...

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1 1 Statistical Design and Analysis of Microarray Experiments First Lecture! 1/15/2008 2 Central Dogma: DNA Æ RNA Æ Protein Illustration provided by the National Human Genome Research Institute 3 Microarray Technology ± Monitoring gene expression helps understand the cellular mechanisms for all biological processes. gene function gene network ± Microarray technology allows measuring expression levels (abundance of mRNA transcripts) of thousands of genes simultaneously. 4 Example I: Sawers et al , 2007, BMC Bioinformatics ± The establishment of C4 photosynthesis in maize is associated with differential accumulation of gene transcripts and proteins between bundle sheath and mesophyll photosynthetic cell types. ± Goal : To detect genes that are differentially expressed in Bundle Sheath (B) and Mesophyll (M) cells. 5 Example I: Sawers et al , 2007, BMC Bioinformatics BV M bundle sheath strands mesophyl protoplasts 6 ± A simple method: Isolate cells and perform a microarray experiments to compare the gene expression between the two cells (treatments). Example I: Sawers et al , 2007, BMC Bioinformatics
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2 7 Example I: Sawers et al , 2007, BMC Bioinformatics ± A little more complication: The procedure for extracting mRNA for the two cells are different. The one to extract mRNA from M cells introduces stress. ± Solution : Add two more treatment groups: samples with both M and B cells going through extraction of mRNA with and without stress. Æ B, M, Stress and Total (4 treatment groups) 8 Example II: Jesch et al , 2006, J. Biol. Chem.
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01%20introduction%201_15_08 - Central Dogma: DNA RNA...

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