使用演化足跡法識別轉錄因子目標基因

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童志煌(Jyh-Huang Torng) 查詢紙本館藏

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資訊工程學系

論文名稱

使用演化足跡法識別轉錄因子目標基因
(Mootprinting : Identifying transcription factor binding targetgenes by phylogenetic footprinting)

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摘要(中)

基因表現分析提供許多可能的轉錄因子基因群組，而演化足跡法可用來識別
轉錄因子基因。所以我們開發一個結合尋找具有某種特定功能或構造的片段與演
化足跡法的系統。在輸入一組具有某種特定功能或構造的片段與基因群組，系統
會統計在該片段在人類與老鼠所有基因與基因群上游保守區域的出現情形。系統
可以分辨出有可能是某個轉錄因子調控的基因群組或是沒有關係的基因群組。透
過比較所有基因與基因群組具有某種特定功能或構造的片段分佈情形，本系統可
幫助生物學家識別從基因表現分析得到的群組中，辨識可能是被轉錄因子調控的
基因群組。

摘要(英)

The analyses of gene expression provide lots of possible transcription factor
regulated gene group. It is proven that phylogenetic footprinting method can help to
identify transcription factor binding sites. Our work develops a system that combines
the motif searching and phylogenetic footprinting. After a motif and gene group is
submitted, the system is able to evaluate statistics of motifs appearance in whole genes
and a set of genes upstream conserved region between human and mouse. A
transcription factor-target gene group was used to test the proposed system. The results
present the system can distinguish transcription factor--target gene group from random
gene groups. By comparing motif distribution between whole genes and gene group,
the proposed system is able to help biologists identify possible transcription factor
regulated genes groups form groups of gene expression.

關鍵字(中)

★ 演化足跡法
★ 轉錄因子

關鍵字(英)

★ phylogenetic footprinting
★ transcription factor

論文目次

Expression...........................................................................................3
Regulation of gene expression.....................................................................4
Homologous, Orthologous, Paralogous......................................................4
1.2 Motivation......................................................................................................5
1.3 Goals................................................................................................................5
Chapter 2 Related works........................................................... 7
Chapter 3 Material and Methods...........................................10
3.1 Material.........................................................................................................10
3.2 Methods.........................................................................................................13
Suffix array.................................................................................................13
Chi-Square test...........................................................................................13
Preprocessing..............................................................................................16
3.3 Implementation ............................................................................................17
Chapter 4 Results.....................................................................19
4.1 Web Interface ...............................................................................................19
4.2 Case study.....................................................................................................26
Chapter 5 Summary ................................................................29
References .................................................................................30
Appendix A...............................................................................32

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指導教授

洪炯宗(Jorng-Tzong Horng)

審核日期

2006-7-18

推文