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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/17792

Title: 脊椎動物基因體基因及轉錄因子結合位置的雙向預測工具網
A two-way predicting computational tool website for transcription factor binding site andvertebrate genomes
Authors: Chih-Kai Hsu
許智凱
Contributors: NTOU:Institute of Bioscience and Biotechnology
國立臺灣海洋大學:生物科技研究所
Keywords: 基因體;轉錄因子
E2F;cell cycle
Date: 2009
Issue Date: 2011-07-04
Abstract: 基因的調控是一個相當複雜的機制,如此複雜的調控網路該如何解析一直是功能性基因體學的重要課題。   eMOG (Extraction of Motif or Gene)是我們最近發展出來研究基因調控的工具網頁,利用電腦掃描並分析特定的基因群組,以矩陣計分及統計的方式,來預測調控此基因群組的特定轉錄因子結合位置(transcription factor binding site,TFBS)。同時,我們也反向設計這套工具,讓使用者能由TFBS去預測有可能被TFBS調控的gene cluster,最後我們藉由分析工具的網頁化,方便使用者能選擇某特定基因群組或TFBS自行分析,最終讓使用者獲得分析數據及示意圖檔的網頁超聯結。 在此研究中,我們將以調控細胞週期的E2F家族為例,實際找了115個經Chip-on-chip檢驗後會受E2F直接調控的基因群,然後利用eMOG forward tool分析出調控此115個基因的轉錄因子(E2F、CREB、NF-Y、Nrf-1),最後用eMOG reverse tool分析這4個轉錄因子,並得到27個可能被E2F家族調控的新基因。這27個預測出的新基因到目前為止仍很少被探討,我們在功能性分析後,找到14個基因有文獻證明會影響cell cycle調控、2個基因和membrane receptor有關以及12個功能尚待研究的基因。同時,在多重序列比對這群人類的115個基因之後,我們找到114個老鼠同源基因,以同樣方式進行功能分析之後,我們找到26個新預測出的基因,其中有11個基因文獻已證明會影響cell cycle調控。
Transcriptional control by the transcription factors plays the central roles in the regulation of the gene expression. Given the gene lists involved in a biological phenomenon generated in a gene expression profiling experiment, the commonly asked question is what kind of and how the transcription factors control a battery of genes. eMOG (Extraction of Motif or Gene) is the web tool that we develop to analyze the upstream sequence given a gene list. eMOG scans the upstream sequences of genes and, by judging a probability score, discover the over-represented known transcription factor binding site (TFBS). Furthermore, eMOG allows the users to employ TF names to predict the genes that are potentially regulated by the given TFs. Finally, the user can visualize the TFBS patterns on the upstream sequence of genes using Scalable Vector Graphics (SVG). We use 115 human genes the upstream sequences of which are bound by E2F family, a TF family that regulates the entry of S phase in cell cycle. eMOG revealed four TFBS (E2F, CREB, NF-Y, Nrf-1) that are over-represented in the upstream sequences of those 115 genes. Moreover, we discover another 27 genes that are potentially under the transcriptional control of these four TF by reverse eMOG. Functional analysis of these 27 genes reveals that 14 genes are known to be directly related to cell cycle control and two genes associated with membrane receptor. Interestingly, using the same approach, 26 mouse genes are discovered to be potentially under the transcriptional control of the same four TF by reverse eMOG. The function of 11 out of these 26 mouse genes are known to be related to cell cycle control.
URI: http://ethesys.lib.ntou.edu.tw/cdrfb3/record/#G0M96360009
http://ntour.ntou.edu.tw/ir/handle/987654321/17792
Appears in Collections:[生命科學暨生物科技學系] 博碩士論文

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