研究植物在面對逆境時生理的調控機制大致可以分成兩個方向：一是了解參與逆境反應的基因功能以及其所參與的代謝途徑；二是研究植物在面對空間與時間變化時，如何調整其轉錄機制。目前雖有許多實驗利用微陣列（microarray）技術分析不同基因在逆境時之基因表達變化，並建立相關資料庫。但很可惜地，在目前發表的線上資源中，沒有資料庫可以同時分析不同環境之基因表達變化以及該差異表現基因所參與的代謝途徑。此外在基因轉錄調控方面，轉錄因子在調控上扮演非常重要的角色，但他們仍有許多未知的特性。例如，在阿拉伯芥2296個轉錄因子中，絕大多數轉錄因子在他們目標基因啟動子上的專一結合序列是未知的，另外，只有少數幾篇研究探討轉錄因子在特定環境下的轉錄調控網路。為了解決以上問題，本研究分成兩部分。第一部分，首先收集植物生物逆境、非生物逆境與賀爾蒙處理之微陣列基因表現資料，再以這些資料建立一整合基因表達資料與代謝途徑的資料庫分析平台—EXPath，提供五個主要功能包括：基因搜尋、代謝途徑搜尋、差異表現基因分析、共表達基因分析、代謝途徑與功能豐富度分析、以及功能相互連結的進階分析。第二部分，為了解決基因轉錄調控資訊不足的問題，我們開發一個新的研究方法，應用EXPath的基因表達資料來分析在不同環境下啟動子上之近端與遠端調控因子。我們主要以熱逆境為例子進行分析，結果顯示有9個轉錄因子會專一性地在熱逆境下被啟動，我們將其視為條件特異性轉錄因子(condition specific transcription factors, CsTFs)，其中有4個CsTFs在過去的研究中都被報導與耐熱相關，且會結合在熱休克因子(heat shock elements, HSEs)。但令人驚訝地，另外5個CsTFs目前都僅有零星的研究，我們深信此未被研究的CsTFs可能與植物面對熱逆境時的調控有極大的關係。另一方面，我們也分析CsTFs之共表達基因群的啟動子序列，利用短片段序列的豐富度分析，我們辨認到幾個8-mer序列顯著地出現在CsTFs的共表達基因啟動子上，而且與已知的熱休克因子序列相似。這些結果顯示我們分析在不同環境下啟動子上的近端與遠端調控因子的流程之實用性與高可靠性。

There are two major research directions to understand the regulation mechanisms of plant stresses responsiveness. One is to investigate the functions and metabolic pathways related to stress responsiveness. The other is to study the adjustment of transcription when facing to spatial and temporal changes. To analysis stress-response genes, various microarray-based experiments have been massively preformed to monitor gene expression levels under different stresses, and several related databases have been established. Unfortunately, none of current resources could identify the variation of gene expression profiles and analyze differentially expressed genes (DEGs) and critical stress affected metabolic pathways at the same time. On the other hands, transcription factors (TFs) play crucial roles in the examination of transcription regulation, but still a lot of unknown properties. For example, among 2296 Arabidopsis TFs, most of their corresponding transcription factor binding sites (TFBSs) are unidentified and limit researches focus on dynamic transcriptional regulatory networks depending on different conditions. In order to solve the problems mentioned above, there are two parts in this study. In the first part, we comprehensively collected the public microarray expression data including biotic stresses, abiotic stresses, and hormone treatments and constructed an integrated system for gene expression profiles and metabolic pathways identification. EXPath was developed to provide five major analysis functions, such as Gene Search, Pathway Search, DEGs Search, Pathways/GO Enrichment, Coexpression analysis, and the advanced combination analysis between them. To resolve the shortage information about transcriptional regulation, we set up a novel method for analyzing correlation between trans- and cis- acting elements under various conditions based on expression data of EXPath. The heat stress was used as a case to validate our analysis process. The results indicated that nine transcription factors were highly specific induced by heat stress, and defined as condition specific TFs (CsTFs). Four of nine CsTFs were reported as heat stress transcription factors (HSFs) and could bind on heat shock elements (HSEs). Surprisingly, the other five CsTFs had almost not been studied, we suggested those CsTFs might highly correlate to plant heat adaption. Additionally, based on the motif enrichment analysis in promoters of CsTFs coexpressed gene group, several 8-mer motifs were significantly been recognized and similar to known HSEs. The results demonstrated that the utility and reliability of our methods to discover cis-and trans-acting elements in promoter sequences under different conditions.

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