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DNA Chip Data Interpretation Tools: Genmapp & Dragon View

DNA Chip Data Interpretation Tools: Genmapp & Dragon View. In-Song Koh, M.D., Ph.D. Genomic Research Center for Lung & Breast/Ovarian Cancers College of Medicine, Korea University. cDNA Microarray Schema Duggan et al., Nature Genetics 1999. 1. Array Fabrication. 2. Probe Preparation

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DNA Chip Data Interpretation Tools: Genmapp & Dragon View

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  1. DNA Chip Data Interpretation Tools: Genmapp & Dragon View In-Song Koh, M.D., Ph.D. Genomic Research Center for Lung & Breast/Ovarian Cancers College of Medicine, Korea University

  2. cDNA Microarray SchemaDuggan et al., Nature Genetics 1999 1. Array Fabrication 2. Probe Preparation & Hybridization 3. Data collection, Normalization & Analysis 4. Biological Interpretation

  3. Data from Single Experiment Signal intensity = Spot intensity - Background intensity Log ratio = Cy5 signal intensity / Cy3 signal intensity

  4. Data from Multiple Experiments Gene expression data on m genes for n samples: mxn matrix mRNA samples sample1 sample2 sample3 sample4 sample5 … 1 0.46 0.30 0.80 1.51 0.90 ... 2 -0.10 0.49 0.24 0.06 0.46 ... 3 0.15 0.74 0.04 0.10 0.20 ... 4 -0.45 -1.03 -0.79 -0.56 -0.32 ... 5 -0.06 1.06 1.35 1.09 -1.09 ... Genes Gene expression level of gene 5in mRNA sample 4 = Log( Red intensity / Green intensity)

  5. Clustering Analysis 1. Hierarchical clustering methods 2. K-means methods 3. Self-organizing map (SOM) 4. Neural networks “guilt by association” rule

  6. Cluster 5Cluster 6 Cluster 9

  7. Cluster 5: decrease with progression of carcinogenesis

  8. Dahlquist et al., Nature Genetics 2002

  9. GIGO in Bioinformatics Bioinformatics DataIn Information Out • Garbage In GospelOut: Many people expect. • Garbage In Garbage Out: Truth is • Gospel In Gospel Out: Ideal, Most wanted. • Gospel In Garbage Out: Fire him? Or Ask Him?

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