長久以來，系統生物學研究的終極目標在於理解生物體內部機制的運作，以獲得所需的重要資訊並建構模型工具。功能模組的辨識，其中包含建立分子網路，被認為是了解生物系統中彼此關係及交互作用的基礎。現今的學者嘗試從蛋白質交互作用網路找出功能模組，並以不同的視覺化呈現相關的反應路徑、細胞功能及細胞反應之資訊。目前不論是針對不同功能模組間的關係或是單一模組內間的關係都必須經由人力介入始可完成，使得研究人員與生物學家無法方便且有效地分析並判斷所偵測出來的功能模組是否有意義。所以在本篇論文中我們提供了一個具有互動性的整合系統找尋並視覺化呈現經由分析蛋白質交互作用網路所得到的功能模組。藉由此系統，研究人員可輕易地觀察基因間的相互關係；同時，系統的視覺化呈現可協助他們對所發現到的功能模組做更深入的研究。功能模組與生物反應路徑或基因本體論分類的關聯，描述了ㄧ群基因或蛋白質作用後完成的細胞功能，此外，系統所自動產生的功能模組圖表達了細胞中基因或蛋白質反應時所出現過的路徑、彼此的交互作用關係、在細胞裡的位置、具有的功能以及參與的反應，以呈現基因或蛋白質在細胞中作用的概觀結果。整體而言，本論文開發一個能自動找出基因功能模組，幫助使用者有效率地進行分析並找出有用知識的系統。

　Assimilating the intrinsic workings of biological mechanism to derive prerequisite knowledge and modelling tools has long been an ultimate goal in systems biology. Identification of functional modules, which constitute the building blocks of molecular networks, serves as the cornerstone for the understanding of the relationships and interactions between various parts of a biological system. Researches to date have attempted to uncover modules from protein interaction networks and correlated them with pathways and cellular functions or processes through different visualisations. The current depictions of the relationships of inter- and intra-modules, however, are done manually and the cellular interactions among genes or proteins are not being captured in a single clear global snapshot. All these have impeded the medical researchers or biologists’ ability to efficiently analyse and comprehend the detected functional modules. In this research, we endeavour to provide an interactive and integrated system to discover and visualise functional modules identified from protein-protein interaction networks. With our proposed system, researchers can gain valuable biological insights into the inter-relations of their genes of interests for further analysis via discovered functional modules and the unique visualisations. The association of modules to biological pathways or Gene Ontology classifications delineates the impacts a group of genes or proteins may have in performing cellular functions. At the same time, the auto-generated interactive module group diagram, elucidating genes or proteins’ travelling paths, interacting partners, interaction sites, functional roles and involved biological processes all at once, presents globally the inner workings within a cell. Overall, we have developed an automated functional module discovery application that allows efficient analysis and knowledge discovery.

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