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標題: 利用高通量定序資料預測老鼠微核醣核酸轉錄起始位置
Using high-throughput sequencing data to identify the transcriptional start sites of mouse microRNAs
作者: 方浩宇
Fang, Hao-Yu
Contributors: 謝立青
基因體暨生物資訊學研究所
關鍵字: 微核醣核酸;轉錄起始位置;老鼠;支援向量學習機
miRNA;transcription start site (TSS);Support Vector Machine (SVM);mouse
日期: 2013
Issue Date: 2013-11-19 12:02:07 (UTC+8)
Publisher: 基因體暨生物資訊學研究所
摘要: 微核醣核酸 (microRNA; miRNA) 是一種非編碼小片段核醣核酸 (non-coding small RNA),它的主要功能為抑制訊息核醣核酸 (messenger RNA; mRNA) 的轉錄進而影響許多蛋白質表現。確認微核醣核酸的轉錄起始位 (transcription start sites; TSSs) 對於研究微核醣核酸上游調控網路很重要。已經有一些鑑定人類微核醣核酸轉錄起始位的研究正在發展中,在本研究我們則專注在老鼠微核醣核酸轉錄起始位位置的預測,因為預測老鼠微核醣核酸轉錄起始位對於微核醣核酸上游調控網路演化的研究將有很大的助益。在這個研究裡我們整合了 Cap Analysis of Gene Expression (CAGE) 與 Transcription Start Sites Sequencing (TSS Seq) 等這些利用高通量定序得到有關基因起始位置的研究資料,並利用支援向量學習機 ( Support Vector Machine; SVM) 方法有系統地預測老鼠微核醣核酸轉錄起始位。實驗的最後我們可以利用支援向量學習機法找到可能含有轉錄起始位的區域,並利用表現序列標籤 (Expression Sequence Tag; ESTs) 與序列保守性 (Sequence Conservation) 作為判斷轉錄起始位的依據。
MicroRNAs (miRNAs) are non-coding small RNAs that inhibit protein coding gene expression by hybridizing with messenger RNAs (mRNAs). MiRNAs are involved in a lot of diverse biological processes and various diseases. To identify miRNA transcription start sites (TSSs) is important for studying the upstream regulatory networks of miRNAs. Up to now the studies regarding miRNA TSS identification are all focus on human miRNAs. We are interested in other species and our aim in this study is to identify mouse miRNA TSSs and the result would contribute to understanding the evolution of upstream regulatory networks of miRNAs.
In this study, we integrated two types of high-throughput sequencing data, i.e. transcription start sites sequencing (TSSseq) and Cap Analysis of Gene Expression (CAGE), as the evidence of miRNA TSSs. A machine-learning-based Support Vector Machine (SVM) was developed to identify mouse miRNA TSSs. In addition, we also incorporated the ESTs (expression sequence tag) and sequence conservation information to provide evidence for mouse miRNA TSSs.
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