請用此 Handle URI 來引用此文件: http://hdl.handle.net/11455/60840
標題: 利用染色質特徵及轉錄因子的結合活性建立轉錄表現量之模型
Modeling transcript expression by using chromatin features and transcription factor binding activity
作者: 袁偉勝
Yuan, Wei-Shen
關鍵字: chromatin
染色質
transcription factor
transcription expression
Support Vector Regression (SVR)
轉錄因子
轉錄表現量
支持向量迴歸
出版社: 基因體暨生物資訊學研究所
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摘要: 組蛋白修飾作用 (Histone modification) 在許多生物學的過程中扮演重要的角色,包括轉錄調節、複製 (replication) 、選擇性剪接 (alternative splicing) 、DNA修復 (repair) 、細胞凋亡 (apoptosis) 和基因沉默 (gene silencing) 等過程,而組蛋白修飾作用對基因轉錄的正負調控已被證實是和修飾的位點及型態有關,例如 H3K4me3 及 H3K4me1 是和基因轉錄的正調控有高度相關,而 H3K27me3 則是和基因轉錄的負調控有關。轉錄因子 (transcription factor) 是指能夠結合在某基因上游特異核苷酸序列上的蛋白質,這些蛋白質能藉由調控核糖核酸聚合酶與 DNA 模板的結合來影響基因的轉錄。因此為了研究組蛋白修飾作用及轉錄因子和基因表現量之間的關係,我們利用支持向量迴歸 (Support Vector Regression, SVR) 方法,藉由染色質的特徵以及轉錄因子位於 DNA 的轉錄起始位置及第一個內含子 (intron) 周圍的訊號做為特徵值,建立出一個模型,經由此模型可以預測出基因的表現量,此外,我們也發現了當利用越靠近轉錄起始位置上的標記訊號來做為特徵值時,對預測準確度的貢獻也就越大,而使用第一個內含子上下游位置上的標記訊號來做為特徵值,預測效果也有一定之水準。
Histone modification plays an important role in biology processes including transcriptional regulation, replication, alternative splicing, DNA repair, apoptosis, and gene silencing. Histone modification has been demonstrated to regulate gene transcription in positive or negative effect depending on the modification site and type. For example, H3K4me3 and H3K4me1 are correlated with gene activation, whereas H3K27me3 is negatively correlated with gene expression. Transcription factor is a protein that binds to specific DNA sequences in promoter region. The transcription factor can effect gene transcription by regulating the RNA polymerase binding with DNA template. To study the relationship between chromatin feature and transcription expression, we used Support Vector Regression (SVR) to build a model by using both chromatin features and transcription factor binding activity. Moreover, we found that the markers that close to the transcription start site are important for the transcript expression prediction. Using the upstream and downstream of first intron also helps the prediction of transcript expression.
URI: http://hdl.handle.net/11455/60840
其他識別: U0005-2206201102300500
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-2206201102300500
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