隨著大型基因體計畫的進展，大量的生物資料使我們得以更宏觀的角度了解生物問題。而在高通量量測技術中，基因晶片的發展更是近十幾年來應用在基因表現量測的利器。然而從大量的基因表現數據萃取出生物訊息的過程中，往往得先克服許多困難，譬如量測系統的穩定性與可靠性，生物樣品本身的變異與多樣性，以及大量資料的複雜度。如何提升基因晶片分析的可靠性，以及運用現有的分析與注釋工具統整大量資料，以歸納出資料所指出生物現象，就成了運用基因晶片這一利器所必須克服的問題。本論文利用自家點印的基因晶片探討人類細胞的抑癌機制在受到多瘤病毒SV40轉化後的改變，以及蒐集大量的Affymetrix基因晶片資料，以總體分析法(mata-analysis)重新鑑定人類持家基因與組織特異基因的成員與功能。這兩個研究主題同樣循著資料的品管與歸一化得到可靠的量測數值，再依據生物問題設計統計方法與運用生物注釋工具，得到生物結果與拓展新的研究方向。期望從中歸納出的分析概念能有助於之後轉錄體相關的研究，以及應用在其他類型的高通量量測技術，以利功能性基因體學的進展。
多瘤病毒Simian virus 40 (SV40)有能力促使細胞走向癌化，而與其相關的研究成為了近代我們對癌症形成機制的知識基礎。我們運用自家點印的雙色基因晶片，比較了人類肺部纖維母細胞MRC-5以及其受到SV40轉化後的細胞株MRC5CVI，在受到UVB照射以後基因表現的改變。我們先以functional enrichment analysis總覽兩株細胞在照射UVB以後基因表現的改變，接著我們用expressional correlation的方法從兩組基因晶片實驗篩選出13個表現歧異基因。最後以cell cycle analysis與cell death assay驗證基因表現數據所指出的SV40轉化對抑癌機制的影響。結果發現MRC5CVI失去調控chromosome condensation、DNA repair、cell cycle arrest，以及apoptosis等相關基因，但保有在受到輻射照射以後上調oxidative phosphorylation相關基因表現的能力。然而MRC5CVI雖然無法調控apoptosis基因的表現，在照射UVB以後的細胞死亡狀況卻顯著地比MRC-5來得高，此一結果與過去研究認為癌化細胞對輻射照射的敏感度較低的認知不同，也指出MRC5CVI可能透過transcription-independent的機制走向細胞死亡。後續研究SV40轉化細胞對輻射的敏感度，將可進一步了解敏感化癌症細胞的分子生物學基礎，以提供癌症放射治療新的方向。
從人類基因中鑑定出持家基因(housekeeping gene, HK gene)與組織特異性基因(tissue-selective genes, TS gene)可以幫助之後基因功能研究的進展，以及組織相關疾病的了解。然而之前的研究侷限於能夠獲取的正常人類組織基因表現的資料不足，使得篩選出來的HK與TS genes缺乏代表性，也間接導致後來關於這兩種基因結構研究的矛盾。我們利用實驗室架構的基因晶片資料庫M2DB，匯整出跨越104組實驗、43種人類組織，總計1431筆Affymetrix 基因晶片原始資料以進行總體分析。除了發展出新的數值與方法來評估基因表現與探討過去研究的優缺點，並指出對於每一種組織，至少需要10個以上的樣本才能明確地鑑定組織的轉錄體。基於這些進展，我們鑑定出2,064個HK genes與2,293個TS genes，並以functional enrichment analysis探討這些基因的功能。結果顯示HK genes與重要的基礎細胞功能有關，而TS genes則與相對應的組織功能高度呼應。比較本研究與過去鑑定的HK genes的差別，我們指出造成過去鑑定的HK genes分歧的一些原因。運用大量資料進行總體分析提升了鑑定出的組織轉錄體的正確性，以及HK genes與TS genes的可靠性。

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