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研究生:鄧詠文
研究生(外文):Yeing-Wen Deng
論文名稱:整合性蛋白質模組資源
論文名稱(外文):IntegDom: an integrated protein domain resource
指導教授:楊永正楊永正引用關係
指導教授(外文):Ueng-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:中文
論文頁數:62
中文關鍵詞:蛋白質模組整合資料庫
外文關鍵詞:protein domainintegrationdatabase
相關次數:
  • 被引用被引用:0
  • 點閱點閱:100
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  • 下載下載:8
  • 收藏至我的研究室書目清單書目收藏:0
目前網路上的蛋白模組資料庫多是以橫向方式整合,多半只有收集蛋白模組的序列相關資訊,若要對具有這些蛋白模組的蛋白質的功能有更進一步的了解,只有序列資訊顯然是不夠的。因此本論文的目的便是以縱向的方式,收集含有這個模組的所有蛋白質在基因體、轉錄體、蛋白體及反應路徑等四個層次的資訊,建置成一個資料庫,稱之為IntegDom。在基因體層次上,IntegDom收集了來自Ensembl這個資料庫所註解的人類的蛋白模組序列資訊,並整合了LocusLink對含有這些蛋白模組的基因註解。除此之外,IntegDom還利用所收集到的蛋白模組序列資訊建立親緣樹,希望能輔助基因功能的預測。在轉錄體層次上,IntegDom整合了來自Unigene收錄的EST的組織資訊,以及來自NCBI的GEO所收集的微陣列資訊供使用者下載。在蛋白體層次上,IntegDom主要收集來自BIND及DIP這兩個資料庫的蛋白交互作用資訊,並以圖形化的方式來呈現蛋白交互作用的網路。最後在反應路徑的層次上,IntegDom則收錄了與蛋白模組相關的反應路徑,也利用圖形化的方式呈現出這些反應路徑共用蛋白質的情形。最後,IntegDom還整合了反應路徑與組織的資訊,這樣的資訊將有助於整合不同的反應路徑,以補目前網路上的反應路徑資料庫只呈現單一反應路徑的缺點。
Most protein domain databases contain mainly sequence information of protein domains. Obviously it is not enough for us to further understand the function of proteins that contain a given domain. The specific aim of my thesis is to construct an integrated domain database in vertical manner. This database, named ‘IntegDom’, will collect genome, transcriptome, proteome and pathway information of each of the protein domains. In genome level information, IntegDom retrieves protein domain sequences from Ensembl database and provide LocusLink annotations of those domain-containing genes. IntegDom also provides phylogenetic tree of protein domain, rather than the full protein. This information may be helpful for function prediction of new genes that contain a specific domain. In transcriptome level, IntegDom integrates tissue information derived from Unigene ESTs sequences and microarray data fetched from GEO database in NCBI. In proteome level, IntegDom collects protein interaction information downloaded from BIND and DIP database and uses a java applet program to display the interaction network. In pathway level, IntegDom lists pathways that are related to a specific domain, and display the component sharing relationship between these pathways. By integrating pathway with tissue information, it will be helpful to integrate different pathways, which is not observed in any other existing databases.
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