建立真核生物體學資料庫分析系統

ODE (Omics Databases of Eukaryotes) to Signaling Pathways

許浩彰(Hao-Chang Hsu)

指導教授 ： 李元綺

臺北醫學大學/醫學院/醫學資訊研究所/碩士(2007年)

https://doi.org/10.6831/TMU.2007.00120

摘要

生物醫學隨著人類基因體計畫階段性完成後已經進入另一個新時代。根據此全基因組的資料並結合生物技術將累積出更多二級性的生物調控網路資訊，包括基因表現量、蛋白質間交互作用等。目前最大的挑戰在於如何處理及整合大量的生物調控資訊，建立生物資訊系統。利用基因體學、蛋白質體學、高效率的篩選(high-throughput screening)等新技術為基礎，也正是達成「系統生物學」的最終目標。如何整合分子與細胞組成、分子交互作用關係、在細胞中的位置及分子在生物體內扮演的角色並進入一個符合生物特性的框架中，加入基因注釋，允許資料儲存、資訊分享是必經之路。在這篇論文中我們嘗試整合蛋白質與蛋白質(protein-protein interaction)、蛋白質與核酸交互作用(protein-DNA interaction)、磷酸化蛋白質體(phosphoproteome)、基因微陣列(microarray)、基因本體論(gene ontology)及基因註釋，發展真核生物體學資料庫分析系統(Omics Databases of Eukaryotes)的平台，並期待以不同的維度分析生物訊息傳遞路徑，找出生理到病理之間的關聯性，嘗試發掘關鍵性的致病基因。

關鍵字

系統生物學 ； 蛋白質與蛋白質交互作用 ； 蛋白質與核酸交互作用 ； 磷酸化蛋白質體學 ； 基因本體論 ； 基因微陣列

並列摘要

Biomedical science had already entered another new era after the completion of the human genome project. With the whole genome data and in combination of advanced biotechnology, it has accumulated a huge mass of secondary structure information of biological regulatory networks, including the gene expression, protein interaction and transcription regulation. The greatest challenge is how to convert all the sporadical pieces of information to reconstruct a biological network of significance. To achieve this goal, we have classified these complicated protein-protein relationships according to their biological context into protein-protein interactions, protein-DNA interactions, phospho-proteomics, transcriptomics, gene ontology, gene-centric annotation and pathways-network among six different species, human, mouse, rat, worm, fly and yeast. This “Omics Databases of Eukaryotes (ODE)” is hence developed for users to search their genes and pathways of interest in our sorted genome-wide databases. ODE contains over 44,263 protein-protein interactions, 10,000 protein-DNA interactions, 9545 phosphorylations and 16,383 expressed human probes (9360 genes) in 79 human tissues and 36114 expressed murine probes (18666 Genes) in 61 murine tissues. This tool is publicly accessible at http://bio.tmu.edu.tw:8080/ODE/.

並列關鍵字

System biology ； Protein-protein interactions ； Protein-DNA interactions ； Transcription factor ； Gene expression ； Pathway discovery

參考文獻

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