2009 CSBB LAB 新生訓練

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系統生物學組介紹。林樹熙主講

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2009 CSBB LAB 新生訓練

  1. 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
  2. 3. Affymetrix analysis system
  3. 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)
  4. 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
  5. 7. 8/7 Histogram Factor 1 Factor 2 ANOVA P
  6. 8. Factor 1 FDR ( false discovery rate ) Factor 2 FDR ( false discovery rate )
  7. 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 -/-)
  8. 10. Factor 1 Rank number = 100
  9. 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 -/-)
  10. 12. Factor 2 Rank number = 100
  11. 13. MAP
  12. 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
  13. 19. Comparative Genomic Hybridization (CGH)
  14. 21. 46XY_ALL ARHGAP6-GTPase activating protein 6   DACH2  bA345E19.2  Link-Analysis
  15. 22. 46XY_ Hypospadia and Oligospermia
  16. 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
  17. 24. Symtems biologial analysis platform in NTHU 11,612 6,434 353,043 11,402 34,435 169,093 59,852 594,111 ……… . Pathways
  18. 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
  19. 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

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