1. Array study discovery-driven Where is the hypothesis ?

2. Cell, Vol. 104, 333–339, 2001

4.  Generation of Biological Theme by Gene Ontology  Pathway - a direct guess  Correlation to other gene list  Co-transcription control hypothesis - a wild guess

5. Gene List (expression) Protein-protein Interaction Function Association GO Pathway MAPPFinder/GoMiner GSCope/DAVID GenMAPP Osprey GSCope DAVID GSCope PathBlazer

6. Generation of Biological Theme by Gene Ontology

7. Gene Ontology Biological Process Molecular Function Cellular Localization

8. Nature Genetics Vol 25, p25

11. http://www.geneontology.org/

12. http://cgap.nci.nih.gov/Genes/GOBrowser

15. http://etbsun2.nlm.nih.gov:8000/perl/gennav.pl

17.  Data ‧經 Drug A 刺激後的 B 細胞於 4 、 8 、 10 ‧經 Drug A 刺激後的 B 細胞於 4 、 8 、 10 小時後分別進行生物晶片分析 小時後分別進行生物晶片分析 (4/0 、 8/0 、 10/0) (4/0 、 8/0 、 10/0) ‧ RNA Dye ‧ RNA Dye Drug Cy3(635nm) Drug Cy3(635nm) Control Cy5(532nm) Control Cy5(532nm)

18. Gene list Gene list Drug A 4 hr /0 hr Drug A 4 hr /0 hr Drug A8 hr/0 hr Drug A8 hr/0 hr Drug A 10 hr /0 hr Drug A 10 hr /0 hr  Data Analysis > 2 & < 0.5

19. DAVID─GO 、 KEGG Pathway http://apps1.niaid.nih.gov/david/

24. MappFinder http://www.genmapp.org/

26. http://discover.nci.nih.gov/gominer/

27. GoMiner

28. GoMiner

32. Pathway - a direct guess

38. Ex. Drug A 4/0

40. ‧ DAVID ─ Pathway (Total Gene) ‧ GenMapp ─  Results Total input Gene ： 1071 Total input Gene ： 1000

41. Correlation to other gene list

42. Lamb et al., Cell, Vol. 114, 323–334 (2003) http://www-genome.wi.mit.edu/cgi-bin/cancer/datasets.cgi

43. 21 genes induced by cyclin D1 & its mutant in MCF-7 human mammary epithelial cells

44. Expression profiles from 190 primary human tumors-search for genes significantly correlated with the level of cyclin D1

45. C/EBP 

46. Promoter Analysis

47. Co-transcription control hypothesis - a wild guess

49. Strategy for expression array-based comparative promoter analysis Werner T. Mamm Genome 10(2):168-75 (1999)

50. human RANTES/CCL5 promoter

51. 共同調控序列 共同調控基因 A B C 老鼠基因體搜尋過濾 胃癌淋巴轉移晶片研究 結果 -9 genes

52. RT-PCR 可能共同調控基因 D E F 基因晶片結果 -36 genes 人類基因體搜尋 基因晶片結果 -30,000 genes New Hypothesis

53. Gene List (expression) Protein-protein Interaction Function Association GO Pathway MAPPFinder/GoMiner GSCope/DAVID GenMAPP Osprey GSCope DAVID GSCope PathBlazer