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9	"Cells are different because of..." Cells are different because of differential gene expression. About 40% of human genes are expressed at one time. Gene is expressed by transcribing DNA into single-stranded mRNA. mRNA is later translated into a protein. Microarrays measure the level of mRNA expression.
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12	"Biological discovery" Biological discovery new and better molecular diagnostics new molecular targets for therapy finding and refining biological pathways Recent examples molecular diagnosis of leukemia, breast cancer, ... appropriate treatment for genetic signature potential new drug targets
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18	Total Solutions for Gene Expression
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25	Array Quality Control
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27	Array Contents: Agilent Catalog Oligo DNA Microarray
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29	Agilent Catalog Oligo DNA Microarray
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34	"Gene Selection" Gene Selection find genes for therapeutic targets avoid false positives (FDA approval ?) Classification (Supervised) identify disease predict outcome / select best treatment Clustering (Unsupervised) find new biological classes / refine existing ones exploration …
35	Journals are Adopting the MGED Standards
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39	"Microarray Services Report" Microarray Services Report 晶片報告 ( I ) Customer Name: Dr. Liu Sample Name: E7 vs.E7 Chip Name: Chip 4 File Name: NCKU-MSP-CR-2004-09-27-01 Date: 2004/09/27
40	"I" I. MIAME (Minimum Information About a Microarray Experiment) Experiment Design: Exp. description: E7 (Cy5) E7 (Cy3) Exp. date: 2004-07-14 ~ 07-15 (實驗時間) Image file: E7: E7.tif E7: E7.tif Scan analysis file: E7: E7.gpr E7: E7.gpr Analysis report file: Chip4_E7.xls Array Design: Array type: Oncogene-Kinase chip (Chip4) Gene information file: chip4_ArrayDesign_genelist.xls Array Location: 12 rows × 16 columns × 3 blocks Chip4_array location.xls
41	"II" II. Analysis Result 1. Array Chip Statistics: Chip4_E7 vs E7_chipStat.xls Vital statistics table Intensity and Ratio Statistics 2. Histogram Analysis
42	"4" 4. Top 15 of Up- and Down-regulated genes list Chip4_E7 vs E7_up&down.xls CGAP Chip4_E7 vs E7_up_top15_CGAP.txt Chip4_E7 vs E7_down_top15_CGAP.txt 5. Microarray Image Figure
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44	"Simple way" Simple way: fixed circle method Advanced: fast marching level set segmentation
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55	Image Analysis & Data Visualization
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61	"Microarray Services Report" Microarray Services Report 實驗分析報告 ( II ) Customer Name: Dr. Liu Chip Number: E7 vs. E7: NCKU-MSP-CR-2004-09-27-01 E7+AS vs. E7: NCKU-MSP-CR-2004-09-27-02 File Name: NCKU-MSP-EXP-2004-09-27-01 Date: 2004/09/27
62	"Clustering Result" Clustering Result: Chip4_E7-E7withAS_Clustering_20040927.xls Change Ratio > 1 Fold Up-regulated Genes: 60 Genes Down-regulated Genes: 75 Genes
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64	"Principal approaches" Principal approaches: Hierarchical clustering (kdb trees, CART, gene shaving) K-means clustering Self organizing (Kohonen) maps Vector support machines Gene Filtering via Multiobjective Optimization Independent Component Analysis (ICA) Validation approaches: Significance analysis of microarrays (SAM) Bootstrapping cluster analysis Leave-one-out cross-validation Replication (additional gene chip experiments, quantitative PCR)
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68	Data Mining Methodology is Critical!
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