系統生物學組介紹。林樹熙主講

2. Analysis pipeline Raw data normalization Statistic Gene expression Differential Gene expression Profile interpretation 臨床病歷 及生醫資料庫 function interaction & linkage map

3. Affymetrix analysis system

5. Gene Expression Array CGMH Dr. Yang Jhih Wei Mouse 430A Chip Nephridium experimentation Day 3 post infection Day 6 post infection Na ï ve Vir d3 Non Vir d3 Vir d3 Non Vir d3 WT 1 5 9 13 17 (#1,#2,#3) (#4,#5) (#1,#2) (#3,#4,#5) TLR2-/- 2 6 10 14 18 (#6,#7,#8) (#9,#10) (#7,#7) (#9,#10) TLR4-/- 3 7 11 15 19 (#11,#12,#13) (#14,#15) (#11,#12) (#13,#14,#15) DKO (TLR2/4 -/- 4 8 12 16 20 (#16,#17,#18) (#19,#20) (#16,#17) (#18,#19,#20)

6. 2-Way ANOVA Factor 1 = {Vir d3 , Non Vir d3} Factor 2 = {WT , TLR2-/- , TLR4-/- , DKO (TLR2/4 -/- )} ANOVA-P Factor 1 , ANOVA-P Factor 2 Factor 1 or Factor 2 Rank number = 100 Factor 1 Factor 2

7. 8/7 Histogram Factor 1 Factor 2 ANOVA P

8. Factor 1 FDR ( false discovery rate ) Factor 2 FDR ( false discovery rate )

9. PCA Factor 1 1 2 3 4 5 6 10 11 12 7 8 9 16 15 17 13 14 18 19 20 Vir d3 Non Vir d3 WT TLR4-/- TLR2-/- DKO (TLR2/4 -/-)

10. Factor 1 Rank number = 100

11. PCA Factor 2 1 2 3 4 5 6 10 11 12 7 8 9 16 15 17 13 14 18 19 20 WT TLR4-/- TLR2-/- DKO (TLR2/4 -/-)

12. Factor 2 Rank number = 100

13. MAP

18. 46XY 46XY 46XY Hypospadia Hypospadia Hypospadia Hypospadia Oligospermia, biopsy confirmed 46XY 46XY 46XX U/A 46XY 46XX 46XY 46XX 46XX 46XX 46XX 46XY 46XY 46XY 46XY 46XY 46XY 46XX 46XX A total of 21 DNA specimens in the 46XY-female family … waiting for the analysis with Affymetrix X-chromosome tiling array U/A U/A U/A U/A 73 21 22 23 25 26 27 44 36 37 35 34 38 40 41 46 45 39 43 78 42 Affymetrix SNP (Single Nucleotide Polymorphism ) Array

19. Comparative Genomic Hybridization (CGH)

21. 46XY_ALL ARHGAP6-GTPase activating protein 6 DACH2 bA345E19.2 Link-Analysis

22. 46XY_ Hypospadia and Oligospermia

23. SNP 6.0 Exon array Association study LOH analysis Copy number analysis QTL analysis Biological network analysis Tissue array biomarkers at DNA level biomarkers at DNA/ mRNA level biomarkers at protein level Diagnosis chip design

24. Symtems biologial analysis platform in NTHU 11,612 6,434 353,043 11,402 34,435 169,093 59,852 594,111 ……… . Pathways

26. Functional linkage map (PPI, GI, protein-DNA) Pathways Disease database (OMIM) Drug-target database Drug-pathway Our Goal SNP database (dbSNP or clinical data) Tissue-specific expression databases (dbEST) Dynamic databases

27. 生醫資料庫 分析平台 臨床知識探勘平台 臨床病歷 及生醫資料庫 FILM 資料庫 ( 基因功能 網路 ) 疾病關連與 藥物 - 靶點作用 網路資料庫 臨床病歷及 生醫資料分析 平台 Gene expression 分析模組 Survival 分析模組 SNP array 分析模組 Text Mining 模組 Pathway analysis 模組 Biomarker and Drug Target prediction 模組 Gene Module analysis 模組