遺傳變異發生在調控元素上之整合系統

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姓名

陳勇安(Yong-An Chen) 查詢紙本館藏

畢業系所

資訊工程學系

論文名稱

遺傳變異發生在調控元素上之整合系統
(REGV Viewer: A web system to integrate genetic variations occurring on regulatory elements and possible affection)

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摘要(中)

單核甘酸多態性(SNP)和短片段重複序列(STR)是最普遍的遺傳變異，廣泛地分布在物種基因體上且形成物種間的差異。除了遺傳變異，仍然有許多調控元素被發現在基因表現上扮演主要或間接的角色，例如轉錄因子結合位點(TFBS)，CpG島(CpG island)上之甲基化位點及微型核醣核酸(miRNA)目標位點。目前沒有任何相關於模擬遺傳變異發生在調控元素上的研究被實作。因此，為了了解並找出如上述之可能的影響，我們發展一個網頁系統工具即REGV Viewer提供一個友善的網頁介面讓使用者能輸入基因名稱或選擇染色體名稱來顯示遺傳變異相關之調控元素的資訊。而且，我們的工具不僅支援邏輯運算的查詢，且顯示大量遺傳變異和調控元素的模擬組合資料、統計圖和圖形化瀏覽。此外，當SNP變異發生在TFBS上，若SNP等位基因頻率(Allele frequency)和TFBS位置權重矩陣被提供，我們的系統也會提供一個參考的分數給使用者去決定和辨別何者因SNP變異而引發之新的TFBS是可能或足夠地重要。

摘要(英)

Single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) are the most common genetic variations which widely spread on the species genome and form the diversities of the species. Except the genetic variations, there are still many regulatory elements such as transcription factor binding sites (TFBSs), DNA methylation sites on CpG islands and microRNA target sites have been found to play the major or indirect roles in regulating gene expression. Currently, there is no any relative work has been down about simulating the genetic variations occurring on regulatory elements. Therefore, in order to understand and find out all the potential affection described above, we develop a web-based system tool namely Regulatory Element and Genetic Variation Viewer (REGV Viewer, REGV for short) which provides a friendly web interface for users to show the information of genetic variations respect to regulatory elements by inputting gene list or selecting one chromosome name. Moreover, our tool not only supports logic operation for querying, but after the submission it also shows the high-throughput simulated and combinative data, statistical graphs and graphical views of genetic variations and regulatory elements. Additionally, when the variations of SNPs occur on TFBSs, and at this time if the SNP allele frequency and TFBS PWMs are provided, our system will also provide a referable score for users to determine and discriminate which new putative TFBSs resulted by SNP variations are potentially or sufficiently significant.

關鍵字(中)

★ 遺傳變異
★ 調控元素

關鍵字(英)

★ regulatory elements
★ genetic variations
★ REGV

論文目次

Chapter 1 Introduction...................................................................................................1
1.1 Background................................................................................................1
1.1.1 Single Nucleotide Polymorphisms.................................................1
1.1.2 Short Tandem Repeats...................................................................2
1.1.3 Transcription Factor Binding Sites................................................2
1.1.4 Methylation Sites on CpG Islands.................................................3
1.1.5 miRNA Target Sites.......................................................................3
1.2 Motivation..................................................................................................4
1.3 Goal............................................................................................................4
Chapter 2 Related Works...............................................................................................5
2.1 Genetic Genome Browser and Database....................................................5
2.2 Biological Genetic Tool.............................................................................6
2.3 Genetic Web-based Browsers comparison.................................................8
2.3.1 General Genetic Genome Browsers comparison...........................8
2.3.2 Other Purpose-specific Tools comparison.....................................8
Chapter 3 Materials and Methods................................................................................10
3.1 Materials..................................................................................................10
3.1.1 Genetic Resource Sequence.........................................................10
3.1.2 Variation Element Data................................................................10
3.1.3 Regulatory Element Data.............................................................11
3.2 Methods....................................................................................................11
3.2.1 System Flow.................................................................................12
3.2.2 Integrate the combinations of Variations (Major Type) occurring on Regulatory Elements....................................................................................14
3.2.3 Process the Variant Type Variations occurring on Regulatory Elements ......................................................................................................14
3.2.4 Create Relative Score between SNP Variations and TFBSs........18
3.2.5 Orthologous Gene Upstream Comparison...................................20
Chapter 4 Implementation............................................................................................21
4.1 Methylation Site Data Preprocessing Agent............................................21
4.2 Data Processing and Database Storage....................................................21
4.3 Web Interface...........................................................................................24
4.4 Statistical Graph and Graphical View......................................................24
Chapter 5 Results.........................................................................................................25
5.1 Web-based REGV Viewer System...........................................................25
5.2 View of Orthologous Gene Upstream Comparison.................................28
5.3 View of SNPs occurring on TFBSs..........................................................30
5.3.1 Statistical view between SNPs and TFBSs..................................30
5.3.2 Comparison between our data and other data set.........................34
5.3.3 Case Study in Scores of SNPs occurring on TFBSs....................34
5.3.4 Phenomena of Scores between SNP Variations and TFBSs........35
5.4 View of SNPs occurring on Methylation Sites on CpG Island................38
5.5 View of SNPs occurring on miRNA Target Sites....................................44
Chapter 6 Summary.....................................................................................................47
6.1 Discussion................................................................................................48
6.2 Future Work.............................................................................................49
References....................................................................................................................50

參考文獻

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指導教授

洪炯宗(Jorng-Tzong Horng)

審核日期

2006-7-18

推文