Array study discovery-driven Where is the hypothesis ?

Cell, Vol. 104, 333–339, 2001

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

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

Generation of Biological Theme by Gene Ontology

Gene Ontology Biological Process Molecular Function Cellular Localization

Nature Genetics Vol 25, p25

 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)

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

DAVID─GO 、 KEGG Pathway

MappFinder

GoMiner

GoMiner

Pathway - a direct guess

Ex. Drug A 4/0

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

Correlation to other gene list

Lamb et al., Cell, Vol. 114, 323–334 (2003)

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

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

C/EBP 

Promoter Analysis

Co-transcription control hypothesis - a wild guess

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

human RANTES/CCL5 promoter

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

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

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