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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 陳倩瑜(chien-yu chen) | |
| dc.contributor.author | yu-shing lai | en |
| dc.contributor.author | 賴昱行 | zh_TW |
| dc.date.accessioned | 2021-06-08T01:02:28Z | - |
| dc.date.copyright | 2014-10-03 | |
| dc.date.issued | 2014 | |
| dc.date.submitted | 2014-09-30 | |
| dc.identifier.citation | Ansorge, W.J., 2009. Next-generation DNA sequencing techniques. New biotechnology 25, 195-203.
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/18383 | - |
| dc.description.abstract | 近年來RNA定序(RNA-sequencing)已經成為量測基因表現量的重要技術，然而，現有定序技術存在幾種偏差(bias)，這些偏差導致轉錄序列所產生的定序讀段 (read) 在轉錄序列上的分布並非是均勻分布的 (uniform distribution)，這會導致轉錄序列的某些轉錄序列區段(region)存在的定序讀段量較高，某些區段較低。此類由於定序技術偏差而造成轉錄序列區段上讀段分布不均的現象，可能大大影響轉錄序列定量的準確性，進而影響基因表現量差異分析的結果。為此，本研究比較五種量度基因表現差異的方法，其中包含以全長轉錄序列(full-length)量度表現差異的方法和以轉錄序列區段(segment-based)量度表現差異的方法，其結果顯示，其中一種以轉錄序列區段計算表現量差異的方法SRA較傳統上以全長轉錄序列計算表現量差異的方法好，尤其是在轉錄序列表現量很低的時候，其定量準確性相對高出很多。因此本研究最後建議，RNA定序的使用者將來若希望將低表現量的基因納入計算的話，可以考慮使用以轉錄序列區段的定量方式(SRA)進行基因表現差異的量測。 | zh_TW |
| dc.description.abstract | RNA sequencing (RNA-seq) technology is an essential tool for investigating transcript (gene) expression and has been widely suggested by many recent studies. However, several potential biases result in the situation that the read sampling is not uniformly distributed in different regions of a transcript. Such position biases might largely affect the accuracy of quantification methods in correctly estimating transcript (gene) expression, and thus is a critical issue to tackle in differential expression analysis of RNA-seq data. In this study, five quantification methods of producing transcript differential scores across two experimental conditions are presented and compared. Differential scores across two experiments were constructed using the full-length transcripts and the segments of each single transcript, respectively. Results revealed that the segment-based method, SRA, can report more consistent transcript differential scores with the estimated scores from microarrays than the full-length approach, especially when the transcript (gene) expression is low. The analyses conducted in this study suggested the RNA-seq users to employ the differential scores integrated from multiple segments for discovering differential genes, especially when the transcript (gene) expression is considerably low. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-08T01:02:28Z (GMT). No. of bitstreams: 1 ntu-103-R01631008-1.pdf: 3003437 bytes, checksum: bb7128235f11f267056a5d39163d63ff (MD5) Previous issue date: 2014 | en |
| dc.description.tableofcontents | 致謝 i
摘要 ii Abstract iii 目錄 iv 圖目錄 vi 表目錄 viii 第一章 前言 1 第二章 研究目的 4 第三章 文獻探討 6 3.1微陣列晶片 6 3.2次世代定序 6 3.2.1 Illumina定序技術 7 3.2.2 RNA定序 7 3.2.3 單端定序讀段與雙端定序讀段 9 3.2.4 鏈特異性RNA定序 9 3.3 定序讀段回貼工具 10 3.4 轉錄序列定量 12 第四章 材料與方法 14 4.1 RNA定序與微陣列晶片 14 4.2 參考序列組 15 4.3 序列回貼及表現量定量 16 4.4 五種定義表現量差異的方法 16 4.5 驗證五種方法之優劣 19 4.6 不同區段長度表現量差異探討 19 4.7 含有探針序列區段對於微陣列相關性探討 20 4.8 qPCR驗證 20 第五章 結果與討論 21 5.1 定序讀段前處理 21 5.2 轉錄序列區段多樣性 23 5.3 五種表現量差異方法比較 25 5.3.1探討在平台之間表現量差異值不一致的原因 26 5.4 消除RNA定序低表現量影響 29 5.4.1 提高FPKM或PRKM的閥值 29 5.4.2 提高區段對 (segment pair) 數目 31 5.4.3 使用人類資料進行方法的比較 36 5.5 轉錄序列表現量高低的影響 39 5.6 區段多樣性的影響 43 5.7 不同區段長度影響 46 5.8 含有探針序列的區段對於微陣列相關係數之影響 47 5.9 qPCR結果驗證 47 第六章 結論 50 文獻 52 附錄1 程式化腳本 55 附錄2 各分析流程檔案程式碼 70 附錄3 total-seq重複性高的定序讀段 130 | |
| dc.language.iso | zh-TW | |
| dc.title | 利用多序列區段增進轉錄體定序資料之
差異表現分析的可靠性 | zh_TW |
| dc.title | Segment-based quantification of differential expression in RNA-seq data | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 103-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 劉力瑜(Li-yu D Liu),吳君泰(June-Tai Wu),許如君(Hsu, J. C) | |
| dc.subject.keyword | 次世代定序,區段表現量差異,低表現量, | zh_TW |
| dc.subject.keyword | next generation sequencing,segment-based differential expression,low transcript (gene) expression, | en |
| dc.relation.page | 133 | |
| dc.rights.note | 未授權 | |
| dc.date.accepted | 2014-10-01 | |
| dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
| dc.contributor.author-dept | 生物產業機電工程學研究所 | zh_TW |
| 顯示於系所單位： | 生物機電工程學系 | |
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