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 Schema Duggan 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 …
Genes 3
Gene expression level of gene 5 in mRNA sample 4
= Log( Red intensity / Green intensity)

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

6. Cluster 5 Cluster 6 Cluster 9

7. Cluster 5: decrease with progression of carcinogenesis

10. Dahlquist et al.,
Nature Genetics 2002

33. GIGO in Bioinformatics
Data In
Information Out
Garbage In Gospel Out: 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?