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研究生:蕭丞凱
研究生(外文):Cheng-Kai Shiau
論文名稱:應用小鼠EST資料庫於發育關鍵基因探索
論文名稱(外文):Developmental significant genes discovery in silico with mouse EST dataset
指導教授:林文昌林文昌引用關係楊永正楊永正引用關係
指導教授(外文):Wen-Chang LinUeng-Cheng Yang
學位類別:碩士
校院名稱:國立陽明大學
系所名稱:生物化學研究所
學門:生命科學學門
學類:生物化學學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:英文
論文頁數:49
中文關鍵詞:生物資訊表現序列標記發育
外文關鍵詞:bioinformaticsESTdevelopment
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  • 點閱點閱:84
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為了能找尋發育調節關鍵基因,我們使用RIKEN的小鼠EST資料。由於RIKEN的EST資料是從小鼠的所有發育時期的胚胎細胞產生出來的,資料的來源完整性足夠且一致,因此我們以RIKEN的EST資料作為我們研究的起始資料。我們也使用RefSeq資料當作基因的標準,並且利用扣除法與A-C test統計方法,以PERL程式語言開發出一套簡單的基因挑選系統,我們也利用此系統挑出了225筆只於小鼠胚胎時期有EST而成熟時期沒有EST的基因。之後我們再把這225筆資料與MGI的GXD資料庫的TS28(小鼠成熟時期)資料去做比較,在這225筆基因中,有162筆 (佔225筆的72%) 在GXD的TS28資料裡比對不到,意即這162筆基因很有可能就只會表現在小鼠的胚胎時期。之後我們再從中挑選出21個只會在小鼠發育第七天或第十五天才會表現的基因,並設計引子,以聚合酶鍊反應來做分子生物學上的驗證。總結我們開發的系統,利用生物資訊的技術,以EST為資料來篩選出最有可能只會在胚胎發育階段才會有表現的基因。希望我們開發的系統可以幫助發育生物學家快速地找出胚胎發育的關鍵基因而解開胚胎發育之謎。
To find out the significant genes for development, we use RIKEN mouse EST data because of the consistency in the developmental stages libraries. Using mouse RefSeq data as gene reference, we develop a simple web interface by a subtraction strategy and the A-C test. We retrieved 225 significant RefSeq genes that have more than 1 record of EST in embryonic stage but none in adult. Comparing with gene expression database (GXD), 162 (72% of 225) genes are still having no expression evidence in adult library according to EST and GXD. By using GO term to assist functional annotation, we pick 21 genes, which have EST present in mouse 7-day or 15-day embryonic libraries. We then perform RT-PCR to validate these 21 genes selected from computational results, and the PCR results correlate to the computational results.
In conclusion, by performing bioinformatic technology, our system can help developmental biologists to retrieve developmental significant genes according to EST data. And the information generated from our system can assist developmental biologists to find out the keys and mechanisms of developmental process and cellular differentiation.
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