自艾菲矩陣公司表現序列晶片計算信息核糖核酸同型體的表現量的新方法

Abstract

選擇性剪接(alternative splicing)是一種核糖核酸進程(RNA process)，用以使同一基因產生多樣不同的轉錄產物(transcripts)。此一機制發生於真核生物與病毒。人類的基因中，超過50%的轉錄產物進行選擇性剪接，而這機制和疾病發生、治療方法有高度的相關性。不同的信息核糖核酸同型體(mRNA isoform)表現量可能影響不同的蛋白質同型體表現量。 如何利用表現序列晶片分析信息核糖核酸同型體的表現量，是相當重要的。特別是現今艾菲矩陣公司表現序列晶片已被廣為使用，可以偵測基因和表現序列的表現量。 本論文提出一種方法，能自艾菲矩陣公司表現序列晶片計算信息核糖核酸同型體的表現量。該方法使用三個矩陣P、E、I，以P、E矩陣經由OSA計算出IE矩陣。結果顯示，我們的計算和逆轉錄連鎖反應實驗(RT-PCR)驗證的結果符合。

Alternative splicing is a RNA process generating multiple different transcripts from the same gene. It occurs in eukaryotes and viruses. Alternative splicing is generally believed to occur more than 50% of actively transcribed human genes and thus is highly relevant to disease and therapy. Different mRNA isoforms expression might cause different protein isoforms expression. How to use high throughput exon array to analysis different mRNA isoforms expression is very important. Recently, Affymetrix GeneChip®Exon Array has become one of the most popular technologies for profiling gene expression and exon expression. This thesis proposes and implements a method to determine different isoform expression of the exon array. Our method uses matrix P (Probeset expression data) and matrix E (Exon profile) to compute matrix I (Isoform expression) by Orthogonal Simulated Annealing algorithm (OSA), and our calculated results agree approximately with RT-PCR validation.