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系統識別號 U0026-0708201415582200
論文名稱(中文) 開發整合微核糖核酸預測資料庫的系統來辨識被一組微核醣核酸共同調控的標靶基因之研究
論文名稱(英文) Integrating multiple microRNA prediction databases to identify specific target genes co-regulated by a set of microRNAs
校院名稱 成功大學
系所名稱(中) 生物資訊與訊息傳遞研究所
系所名稱(英) Insitute of Bioinformatics and Biosignal Transduction
學年度 102
學期 2
出版年 103
研究生(中文) 姜權芳
研究生(英文) Chuan-Fang Chiang
學號 z26011063
學位類別 碩士
語文別 中文
論文頁數 53頁
口試委員 指導教授-曾大千
口試委員-王育民
召集委員-劉宗霖
中文關鍵字 微核醣核酸  預測工具  共同調控 
英文關鍵字 microRNA  prediction tool  co-regulation 
學科別分類
中文摘要 微核醣核酸(microRNA, miRNA)是一個不會被轉譯成蛋白質的小片段長度(~22核苷酸長)的核醣核酸,同時,miRNA不僅可以藉由種子序列(Seed region)和mRNA的3’非轉譯區(3’-untranslated region, 3’- UTR)互補,並抑制mRNA的蛋白質合成,造成微核醣核酸會影響到許多的生理功能,包括:細胞分化、細胞增生、細胞死亡、細胞生長等等。在過去的研究文獻也指出,由於單一的微核醣核酸會影響到上千個的基因,因此,在生物實驗驗證微核醣核酸的標靶基因上,會顯得十分耗成本及時間,所以,隨著時間的演進,微核醣核酸預測基因的資料庫也隨之而發展,藉由電腦化的計算來辨別其有可能被微核醣核酸調控的基因,目前為止,有很多實用的線上預測工具,如:miRanda、TargetScan、DIANA-microT、miRDB等等,但是,每個工具所預測的基因之結果不盡相同,因此,我們整合了線上微核醣核酸預測基因的工具來尋找真正被微核醣核酸調控的基因,除此之外,近年來有研究指出,多個miRNA也會針對單一基因進行共同調控,進而影響細胞的行為,所以,我們也提供額外的功能讓研究學家探討miRNA及基因之間的共同調控關係,並提供miRNA及基因表現量分析和新的miRNA預測基因之分數讓使用者可以更快速找到其符合的結果,總而言之,本研究所開發的整合微核醣核酸預測資料庫的系統提供方便、簡單、實用的功能讓研究學家使用。
英文摘要 MicroRNA (miRNA) is a class of noncoding small RNAs about 22 nt in length which bind to the 3’ untranslated region (UTR) of target genes. They have been found to regulate genes involved in diverse biological functions. MiRNAs also prevent protein synthesis by inhibiting translation or inducing target degradation. In the past, the process of validating a potential miRNA target in the laboratory is time consuming and costly. Therefore, computational prediction of miRNA targets is a critical initial step in identifying interactions of miRNA and mRNA target for experimental validation. Till now, several useful prediction tools for miRNA target genes have been developed. For example, miRanda and TargetScan both predict miRNA target genes by the rules of seed match and 3’ UTR pairing, DIANA-microT develops a dynamic programming algorithm to calculate scores based on the affinity of the interactions between miRNAs and gene targets ,and miRDB makes miRNA target predictions using SVM and features extracted from a large microarray training dataset. Therefore, we integrate these prediction databases to find the real target genes. And we not only provide kinds of databases for users to choose, but also supply user data to predict target genes in our website. In addition to finding important miRNA and mRNA interaction, we also find each target gene that co-regulated by several miRNAs through data from users. Moreover, we provide researchers with combining the mRNA expression data and miRNA and analyzing their correlation. In summary, our web site is easy and friendly to use for researchers.
論文目次 中英文摘要 i
誌謝 v
目錄 vii
表目錄 ix
圖目錄 x
附錄目錄 xi
Chapter 1 背景介紹 1
1.1 基因之調控 1
1.2 微核醣核酸之介紹 1
1.3 微核醣核酸之生物合成 2
1.4 微核醣核酸與基因之後轉錄抑制 3
1.5 整合微核醣核酸預測基因的工具 3
1.5.1 miRSystem 4
1.5.2 miRWalk 5
1.5.3 miRecords 5
1.6 研究動機 6
Chapter 2 資料蒐集及方法 8
2.1 系統的工作流程 8
2.2 miRNA及基因資料庫蒐集與處理 9
2.2.1 TargetScan 9
2.2.2 miRanda 10
2.2.3 miRDB 10
2.2.4 Diana-microT 11
2.2.5 miRTarbase 11
2.3 miRNA及基因表現量資料組蒐集與處理 11
2.4 皮爾森相關係數分析 12
2.5 分數及權重計算方式 13
2.6 系統配備及環境 15
Chapter 3 實驗結果與分析 18
3.1 分數及權重計算之結果 18
3.2 驗證其他整合工具與N分數比較之結果 20
3.3 miRNA及基因之間的共同調控關係 22
3.4 經實驗驗證的miRNA及基因有相互作用之結果 23
3.5 基因表現量資料之分析結果 24
Chapter 4 討論 26
Chapter 5 參考文獻 30
附表 34
附圖 35
附錄 51
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