果蠅基因交互作用之視覺化與網絡分析平台建置

Construction of an Online Network Visualization and Analytic Platform for Fly Gene Interactions

黃建霖

指導教授 ： 唐傳義 ； 廖崇碩

國立清華大學/工學院/工業工程與工程管理學系/碩士(2012年)

摘要

果蠅許多行為模式與人類非常相似，有超過六成的人類疾病基因，在果蠅中存在同源基因，因此果蠅是許多研究中常用的模式生物。許多系統層級的研究，例如生化合成機轉與記憶系統分析，則仰賴基因間交互作用資訊。近十年來，網路上的生物交互作用資料庫與工具不斷的發展，資料庫和工具的資料特性和操作介面各自不同，加深了學習與使用的門檻。為了降低資料庫整合的複雜性與簡化操作介面，我們以果蠅為模式生物建置了一個網路工具平台：PCmap (Post-genomic connectivity map viewer)，整合相關的基因相互作用資訊。PCmap提供了易於擴展及操作的圖形化網路介面，整合了分散於不同資料庫的果蠅基因交互作用資料，包括蛋白質交互作用、蛋白質-RNA的交互作用以及Pathway等資訊，這些資料能輔助生物學家對果蠅相關實驗的結果進行分析。PCmap也是目前第一個有路徑搜尋、規劃功能以及基因網絡邏輯運算功能的整合型資料庫。針對分析結果也提供用戶輸出基因名單，並產生整合性的報告頁面，呈現位於不同資料庫和工具的資料頁面供使用者參考。經由生物實驗找出來的少量關鍵基因可透過PCmap尋找相連的基因組，並利用PCmap提供的分析、過濾工具，對基因名單進行分析及篩選，快速且有效的聚焦於有研究價值的基因名單進行後續分析。PCmap可以於(http://pcmap.life.nthu.edu.tw)免費使用。

關鍵字

基因交互作用 ； 蛋白質交互作用 ； 視覺化網路 ； 長期記憶 ； 果蠅

並列摘要

A number of the behaviors of the fly are similar to those of humans. More than 60% of human disease homologous genes have been found within fly. Therefore, the fly can be considered a proper model organism for numerous systematic research fields, such as studies of biochemical synthesis and memory formatting mechanisms. To study the large scale systematic problems, strategies based on gene-gene interaction become a feasible solution. For this reason, more and more databases and tools for biological interactions have been developed in the last decade. However, highly data type inconsistence and user interface diversities are commonly found in those tools.
In order to increase the usability and integrate those of inconsistent data, we developed PCmap (Post-genomic connectivity map viewer) by using fly as the model organism. PCmap provides an easy-to-use graphic user interface and a comprehensive querying system from different data sources including protein-protein/protein-RNA interaction datasets and metabolic pathway databases which can assist systematic studies of fly. Moreover, PCmap is the first integrated database which provides fully functionalities of path finder of interaction network and logical operations of different maps. With the help of PCmap’s information retrieval modules, researchers can enlarge their research gene sets based on a few core genes discovered by wet-lab experiments.
We believe that PCmap is not only the visualization tool but a network analyzer which can provide powerful applications to wet-lab researches. PCmap is now freely available on (http://pcmap.life.nthu.edu.tw).

並列關鍵字

Gene-gene interaction ； protein-protein interaction ； network visualization ； long-term memory ； Fly

參考文獻

2. Sutton MA, Schuman EM: Dendritic protein synthesis, synaptic plasticity, and memory. Cell 2006, 127(1):49-58.

3. Martinez JL, Jr., Derrick BE: Long-term potentiation and learning. Annual review of psychology 1996, 47:173-203.

4. Kandel ER: The molecular biology of memory storage: a dialogue between genes and synapses. Science 2001, 294(5544):1030-1038.

5. Chen CC, Wu JK, Lin HW, Pai TP, Fu TF, Wu CL, Tully T, Chiang AS: Visualizing long-term memory formation in two neurons of the Drosophila brain. Science 2012, 335(6069):678-685.

7. Letsou A, Bohmann D: Small flies--big discoveries: nearly a century of Drosophila genetics and development. Developmental dynamics : an official publication of the American Association of Anatomists 2005, 232(3):526-528.