了解和分析複雜的基因調控-表達-回饋的過程，必頇以系統生物學觀念，藉由運用高通量檢 測及資訊分析等方法來完成。微陣列實驗及其高通量檢測技術興起，為系統生物學奠定了 一個重要的里程碑。 本研究利用外顯子微陣列晶片(Exon array)高通量基因分析實驗，篩選 Sw480、Caco2、Ht29 細胞株經由 EGF 刺激和 Cetuximab 阻斷後，對於 EGFR 下游外顯子基因的啟動或其它路徑 的變化基因。利用 SAM 的生物晶片顯著分析方法，篩選出 3052 個有顯著意義變化的基因， 並做基因功能分類以及經 KegArray 軟體處理對應到 KEGG 路徑的列表，找出各細胞株之 間相對的特異性。再利用 R 套件畫出熱相圖並用歐氏距離和 Pearson 相關係數計算出每株 細胞控制組和實驗組之相似性。 經由 KegArray 聯結 KEGG 生物訊息路徑資料初步比對後，發現 Sw480、 Ht29 、Caco2 細胞株經 Cetuximab 阻斷 EGFR 之後於 EGFR-Ras 路徑的差異性以及不同下游子生物路徑 的改變情形。 未來在我們研究當中，希望可以針對大腸直腸癌細胞經 Cetuximab 阻斷 EGFR-Ras 路徑後 之整體訊息路徑變化以及相關關鍵基因進行分析，並觀看其各子路徑中的基因變化。希望 可以藉由系統生物學的概念整合出關鍵基因在不同的生物路徑中複雜的關係與交互作用， 並探討基因分子訊息路徑與上下游基因之調控機制。 In order to understand the complexity of regulation, expression and feedback mechanism of genes, the methodology of system biology through the high-throughput analysis and information analysis must be utilized to elucidate the gene regulation network. The advance in microarray experiment and its high throughput analysis has set up an important milestone in the system biology. In this study, we used the exon array and high throughput data analysis software developed by Partek Corporation to observe the change of EGFR downstream targets after EGF and Cetuximab blockade in Sw480, Caco2 and Ht29 cells. By using SAM biochip significance analysis method, 3052 significantly different genes were selected. These genes were grouped by different functions and relativity between different cell lines by correlating these genes with KEGG mapping .We analyze the heat map of each cell line before and after stimulation by using R package. We also compare the difference of control and experiment group and similarity between other two groups by using Euclidean distance and Pearson correlation. Using KegArray in conjunction with KEGG biological information pathway data，we found the different downstream pathway transformation.of the Sw480、 Ht29 、Caco2 cell line after treatment with Cetuximab to block EGFR and EGFR-Ras pathway. In the furture, we hope to detect different gene mutation after treated with Cetuximab using colon cancer cell lines and observe gene alteration in various EGFR-Ras pathway. We want to integrate complex gene interaction by using system biology. It is valuable to study and investigate the regulation mechanism of upstream and downstream interaction in a pathway.
