果蠅發育過程動態生物網路功能性模組之特性分析研究

Integrative Network Analysis Reveals Dynamic Functional Modules in Drosophila melanogaster Embryonic Development

吳聿笙(Yu-Sheng Wu)

指導教授 ： 阮雪芬

共同指導教授 ： 黃宣誠 ； 歐陽彥正(Yen-Jen Oyang)

國立臺灣大學/電機資訊學院/生醫電子與資訊學研究所/碩士(2010年)

https://doi.org/10.6342/NTU.2010.01344

摘要

胚胎發育是一門已被廣泛研究的學門。然而，發育過程中蛋白質交互作用網路的動態變化卻很少討論到。分子網路是主導分子作用機制的骨幹，結合基因表現數據與蛋白質網路的結合可以幫助我們更了解疾病的分子機制。蛋白質交互作用建構出來的是一個靜態的網絡；結合不同特定生物環境下的基因表現量資料，可以進一步得到動態特性的資訊。在這個研究中，我們提出了一個整合性的網路分析方法。將基因表現量的資訊結合蛋白質交互作用網路及生物功能的註解資料，我們找出主導發育過程中的分子模組。藉由時間序列的基因表現量資訊與果蠅蛋白質網路的整合分析，我們找到不同發育時期的co-expressed 蛋白質網路。結合生物功能註解及動態網路的資訊，藉由統計方法，我們找出各時期的功能性模組。且分析其扮演角色及在不同發育時期表現量上的動態變化。總結，此研究增加了我們對果蠅發育過程一些機制的了解。除此之外，更為未來研究提供了很好的素材。

關鍵字

胚胎發育 ； 時間序列性 ； 共調控 ； 蛋白質交互作用 ； 生物網路 ； 微陣列晶片 ； 果蠅

並列摘要

Embryonic development has been extensively studied, but the dynamics of its protein-protein interaction network remains elusive. As molecular networks represent the backbone of molecular activity within cells, integrative analysis of transcriptomic profiles in the context of protein interaction networks provides opportunities for understanding the molecular mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of the networks. Here, we present an integrative network analysis approach that integrates gene expression profiles with protein-protein interaction and biological function annotations to elucidate molecular modules during developmental processes. Integrating time-series transcriptomic profiles and protein-protein interactome of Drosophila melanogaster, we obtained co-expressed protein interaction networks in different developmental stages during its embryonic development. Applying enrichment analysis for functional dyads and clustering analysis based on network properties or expression profiles, we identified functional modules in each stage and investigated their roles and expression dynamics across stages. In conclusion, this study enriches our understanding of the D. melanogaster developmental process and provides clues for further research.

並列關鍵字

embryonic development ； time-series ； co-expression ； protein-protein interaction ； biological network ； microarray ； Drosophila

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